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| Mainly Beta | ||
| 5 Propellor | ||
| Tachylectin-2; Chain: A; | ||
| SUGAR BINDING PROTEIN | ||
| SUGAR BINDING PROTEIN | ||
Fold relatives
There are either no other non-identical relatives within this fold group or the structural comparisons for this domain have not yet been calculated.
Structural Classification of Proteins
------------------------------------------------------------------------
PDB entry 1TL2
HEADER SUGAR BINDING PROTEIN 14-DEC-98 1TL2
TITLE TACHYLECTIN-2 FROM TACHYPLEUS TRIDENTATUS (JAPANESE
HORSESHOE CRAB)
COMPND MOL_ID: 1;
MOLECULE: TACHYLECTIN-2;
CHAIN: A;
SYNONYM: L10;
OTHER_DETAILS: FORMERLY NAMED L10, NOW TACHYLECTIN-2
SOURCE MOL_ID: 1;
ORGANISM_SCIENTIFIC: TACHYPLEUS TRIDENTATUS;
ORGANISM_COMMON: JAPANESE HORSESHOE CRAB
KEYWDS ANIMAL LECTIN, HORSESHOE CRAB, N-ACETYLGLUCOSAMINE, BETA-
PROPELLER, SUGAR BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR H.-G.BEISEL,S.KAWABATA,S.IWANAGA,R.HUBER,W.BODE
REVDAT 1 15-DEC-99 1TL2 0
JRNL AUTH H.G.BEISEL,S.KAWABATA,S.IWANAGA,R.HUBER,W.BODE
JRNL TITL TACHYLECTIN-2: CRYSTAL STRUCTURE OF A SPECIFIC
JRNL TITL 2 GLCNAC/GALNAC-BINDING LECTIN INVOLVED IN THE
JRNL TITL 3 INNATE IMMUNITY HOST DEFENSE OF THE JAPANESE
JRNL TITL 4 HORSESHOE CRAB TACHYPLEUS TRIDENTATUS
JRNL REF EMBO J. V. 18 2313 1999
JRNL REFN ASTM EMJODG UK ISSN 0261-4189
REMARK 1
REMARK 2
RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REFINEMENT.
PROGRAM : REFMAC
AUTHORS : MURSHUDOV,VAGIN,DODSON
DATA USED IN REFINEMENT.
RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
RESOLUTION RANGE LOW (ANGSTROMS) : 15.0
DATA CUTOFF (SIGMA(F)) : 0.000
COMPLETENESS FOR RANGE (%) : 94.0
NUMBER OF REFLECTIONS : 20892
FIT TO DATA USED IN REFINEMENT.
CROSS-VALIDATION METHOD : THROUGHOUT
FREE R VALUE TEST SET SELECTION : RANDOM
R VALUE (WORKING + TEST SET) : NULL
R VALUE (WORKING SET) : 0.162
FREE R VALUE : 0.202
FREE R VALUE TEST SET SIZE (%) : 10.000
FREE R VALUE TEST SET COUNT : 2072
NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
PROTEIN ATOMS : 1905
NUCLEIC ACID ATOMS : 0
HETEROGEN ATOMS : 75
SOLVENT ATOMS : 158
B VALUES.
FROM WILSON PLOT (A**2) : NULL
MEAN B VALUE (OVERALL, A**2) : 27.80
OVERALL ANISOTROPIC B VALUE.
B11 (A**2) : NULL
B22 (A**2) : NULL
B33 (A**2) : NULL
B12 (A**2) : NULL
B13 (A**2) : NULL
B23 (A**2) : NULL
ESTIMATED OVERALL COORDINATE ERROR.
ESU BASED ON R VALUE (A): NULL
ESU BASED ON FREE R VALUE (A): NULL
ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
RMS DEVIATIONS FROM IDEAL VALUES.
DISTANCE RESTRAINTS. RMS SIGMA
BOND LENGTH (A) : 0.009 ; NULL
ANGLE DISTANCE (A) : 0.025 ; NULL
INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL
H-BOND OR METAL COORDINATION (A) : NULL ; NULL
PLANE RESTRAINT (A) : NULL ; NULL
CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL
NON-BONDED CONTACT RESTRAINTS.
SINGLE TORSION (A) : NULL ; NULL
MULTIPLE TORSION (A) : NULL ; NULL
H-BOND (X...Y) (A) : NULL ; NULL
H-BOND (X-H...Y) (A) : NULL ; NULL
CONFORMATIONAL TORSION ANGLE RESTRAINTS.
SPECIFIED (DEGREES) : NULL ; NULL
PLANAR (DEGREES) : NULL ; NULL
STAGGERED (DEGREES) : NULL ; NULL
TRANSVERSE (DEGREES) : NULL ; NULL
ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
MAIN-CHAIN BOND (A**2) : NULL ; NULL
MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
SIDE-CHAIN BOND (A**2) : NULL ; NULL
SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
OTHER REFINEMENT REMARKS: NULL
REMARK 4
1TL2 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100
THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-1998.
THE RCSB ID CODE IS RCSB000279.
REMARK 200
EXPERIMENTAL DETAILS
EXPERIMENT TYPE : X-RAY DIFFRACTION
DATE OF DATA COLLECTION : NULL
TEMPERATURE (KELVIN) : 289.0
PH : 4.60
NUMBER OF CRYSTALS USED : 1
SYNCHROTRON (Y/N) : N
RADIATION SOURCE : NULL
BEAMLINE : NULL
X-RAY GENERATOR MODEL : NULL
MONOCHROMATIC OR LAUE (M/L) : M
WAVELENGTH OR RANGE (A) : 1.5418
MONOCHROMATOR : NULL
OPTICS : NULL
DETECTOR TYPE : IMAGE PLATE
DETECTOR MANUFACTURER : MARRESEARCH
INTENSITY-INTEGRATION SOFTWARE : MOSFLM
DATA SCALING SOFTWARE : SCALA
NUMBER OF UNIQUE REFLECTIONS : 20896
RESOLUTION RANGE HIGH (A) : 2.000
RESOLUTION RANGE LOW (A) : 15.200
REJECTION CRITERIA (SIGMA(I)) : 2.000
OVERALL.
COMPLETENESS FOR RANGE (%) : 93.7
DATA REDUNDANCY : 4.000
R MERGE (I) : 0.07400
R SYM (I) : NULL
FOR THE DATA SET : NULL
IN THE HIGHEST RESOLUTION SHELL.
HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03
HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43
COMPLETENESS FOR SHELL (%) : 92.2
DATA REDUNDANCY IN SHELL : NULL
R MERGE FOR SHELL (I) : 0.17100
R SYM FOR SHELL (I) : NULL
FOR SHELL : NULL
DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
METHOD USED TO DETERMINE THE STRUCTURE: MIR
SOFTWARE USED: CCP4, SHELXS-97, SHARP
STARTING MODEL: NULL
REMARK: NULL
CRYSTAL
SOLVENT CONTENT, VS (%): 61.0
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14
CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
CRYSTALLOGRAPHIC SYMMETRY
SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
SYMOP SYMMETRY
NNNMMM OPERATOR
1555 X,Y,Z
2555 -Y,X-Y,1/3+Z
3555 -X+Y,-X,2/3+Z
4555 Y,X,-Z
5555 X-Y,-Y,2/3-Z
6555 -X,-X+Y,1/3-Z
WHERE NNN -> OPERATOR NUMBER
MMM -> TRANSLATION VECTOR
CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
RELATED MOLECULES.
SMTRY1 1 1.000000 0.000000 0.000000 0.00000
SMTRY2 1 0.000000 1.000000 0.000000 0.00000
SMTRY3 1 0.000000 0.000000 1.000000 0.00000
SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
SMTRY3 2 0.000000 0.000000 1.000000 24.54000
SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
SMTRY3 3 0.000000 0.000000 1.000000 49.08000
SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
SMTRY2 4 0.866025 0.500000 0.000000 0.00000
SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
SMTRY1 5 1.000000 0.000000 0.000000 0.00000
SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
SMTRY3 5 0.000000 0.000000 -1.000000 49.08000
SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
SMTRY3 6 0.000000 0.000000 -1.000000 24.54000
REMARK: NULL
REMARK 300
BIOMOLECULE: 1
THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR
INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
GENERATING THE BIOMOLECULE
COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
BIOMOLECULE: 1
APPLY THE FOLLOWING TO CHAINS: A
BIOMT1 1 1.000000 0.000000 0.000000 0.00000
BIOMT2 1 0.000000 1.000000 0.000000 0.00000
BIOMT3 1 0.000000 0.000000 1.000000 0.00000
MISSING RESIDUES
THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
M RES C SSSEQ I
VAL A 1
REMARK 500
GEOMETRY AND STEREOCHEMISTRY
SUBTOPIC: COVALENT BOND ANGLES
THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
STANDARD TABLE:
FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
EXPECTED VALUES: ENGH AND HUBER, 1991
M RES CSSEQI ATM1 ATM2 ATM3
PHE A 236 CA - C - O ANGL. DEV. =-15.4 DEGREES
DBREF 1TL2 A 1 236 GB 1256941 D45909 20 255
SEQADV 1TL2 VAL A 129 GB 1256941 ILE 148 CONFLICT
SEQADV 1TL2 TYR A 213 GB 1256941 HIS 232 CONFLICT
SEQRES 1 A 236 VAL GLY GLY GLU SER MET LEU ARG GLY VAL TYR GLN ASP
SEQRES 2 A 236 LYS PHE TYR GLN GLY THR TYR PRO GLN ASN LYS ASN ASP
SEQRES 3 A 236 ASN TRP LEU ALA ARG ALA THR LEU ILE GLY LYS GLY GLY
SEQRES 4 A 236 TRP SER ASN PHE LYS PHE LEU PHE LEU SER PRO GLY GLY
SEQRES 5 A 236 GLU LEU TYR GLY VAL LEU ASN ASP LYS ILE TYR LYS GLY
SEQRES 6 A 236 THR PRO PRO THR HIS ASP ASN ASP ASN TRP MET GLY ARG
SEQRES 7 A 236 ALA LYS LYS ILE GLY ASN GLY GLY TRP ASN GLN PHE GLN
SEQRES 8 A 236 PHE LEU PHE PHE ASP PRO ASN GLY TYR LEU TYR ALA VAL
SEQRES 9 A 236 SER LYS ASP LYS LEU TYR LYS ALA SER PRO PRO GLN SER
SEQRES 10 A 236 ASP THR ASP ASN TRP ILE ALA ARG ALA THR GLU VAL GLY
SEQRES 11 A 236 SER GLY GLY TRP SER GLY PHE LYS PHE LEU PHE PHE HIS
SEQRES 12 A 236 PRO ASN GLY TYR LEU TYR ALA VAL HIS GLY GLN GLN PHE
SEQRES 13 A 236 TYR LYS ALA LEU PRO PRO VAL SER ASN GLN ASP ASN TRP
SEQRES 14 A 236 LEU ALA ARG ALA THR LYS ILE GLY GLN GLY GLY TRP ASP
SEQRES 15 A 236 THR PHE LYS PHE LEU PHE PHE SER SER VAL GLY THR LEU
SEQRES 16 A 236 PHE GLY VAL GLN GLY GLY LYS PHE TYR GLU ASP TYR PRO
SEQRES 17 A 236 PRO SER TYR ALA TYR ASP ASN TRP LEU ALA ARG ALA LYS
SEQRES 18 A 236 LEU ILE GLY ASN GLY GLY TRP ASP ASP PHE ARG PHE LEU
SEQRES 19 A 236 PHE PHE
HET NAG 237 15
HET NAG 238 15
HET NAG 239 15
HET NAG 240 15
HET NAG 241 15
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
HETSYN NAG NAG
FORMUL 2 NAG 5(C8 H15 N1 O6)
FORMUL 7 HOH *158(H2 O1)
HELIX 1 1 TRP A 28 ARG A 31 1 4
HELIX 2 2 TRP A 75 ARG A 78 1 4
HELIX 3 3 TRP A 87 GLN A 89 5 3
HELIX 4 4 TRP A 122 ARG A 125 1 4
HELIX 5 5 TRP A 134 GLY A 136 5 3
HELIX 6 6 TRP A 169 ARG A 172 1 4
HELIX 7 7 TRP A 181 THR A 183 5 3
HELIX 8 8 TRP A 216 ARG A 219 1 4
HELIX 9 9 TRP A 228 ASP A 230 5 3
SHEET 1 A 4 PHE A 231 PHE A 235 0
SHEET 2 A 4 LEU A 7 TYR A 11 -1 N VAL A 10 O ARG A 232
SHEET 3 A 4 LYS A 14 GLY A 18 -1 N GLY A 18 O LEU A 7
SHEET 4 A 4 THR A 33 GLY A 36 -1 N GLY A 36 O PHE A 15
SHEET 1 B 4 PHE A 45 LEU A 48 0
SHEET 2 B 4 GLU A 53 LEU A 58 -1 N VAL A 57 O PHE A 45
SHEET 3 B 4 LYS A 61 THR A 66 -1 N GLY A 65 O LEU A 54
SHEET 4 B 4 LYS A 80 GLY A 83 -1 N GLY A 83 O ILE A 62
SHEET 1 C 4 PHE A 92 PHE A 95 0
SHEET 2 C 4 TYR A 100 SER A 105 -1 N VAL A 104 O PHE A 92
SHEET 3 C 4 LYS A 108 SER A 113 -1 N ALA A 112 O LEU A 101
SHEET 4 C 4 THR A 127 GLY A 130 -1 N GLY A 130 O LEU A 109
SHEET 1 D 4 PHE A 137 PHE A 142 0
SHEET 2 D 4 TYR A 147 HIS A 152 -1 N VAL A 151 O LYS A 138
SHEET 3 D 4 GLN A 155 LEU A 160 -1 N ALA A 159 O LEU A 148
SHEET 4 D 4 THR A 174 GLY A 177 -1 N GLY A 177 O PHE A 156
SHEET 1 E 4 PHE A 184 PHE A 189 0
SHEET 2 E 4 THR A 194 GLN A 199 -1 N VAL A 198 O LYS A 185
SHEET 3 E 4 LYS A 202 TYR A 207 -1 N ASP A 206 O LEU A 195
SHEET 4 E 4 LYS A 221 ASN A 225 -1 N GLY A 224 O PHE A 203
CRYST1 89.460 89.460 73.620 90.00 90.00 120.00 P 31 2 1 6
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.011178 0.006454 0.000000 0.00000
SCALE2 0.000000 0.012907 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013583 0.00000
------------------------------------------------------------------------
Copyright © 1994-2002 The scop authors / scop@mrc-lmb.cam.ac.uk
January 2002
----------------------------------------------------