HEADER SUGAR BINDING PROTEIN 14-DEC-98 1TL2 TITLE TACHYLECTIN-2 FROM TACHYPLEUS TRIDENTATUS (JAPANESE HORSESHOE CRAB) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (TACHYLECTIN-2); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L10; COMPND 5 OTHER_DETAILS: FORMERLY NAMED L10, NOW TACHYLECTIN-2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TACHYPLEUS TRIDENTATUS; SOURCE 3 ORGANISM_TAXID: 6853 KEYWDS ANIMAL LECTIN, HORSESHOE CRAB, N-ACETYLGLUCOSAMINE, BETA-PROPELLER, KEYWDS 2 SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.-G.BEISEL,S.KAWABATA,S.IWANAGA,R.HUBER,W.BODE REVDAT 5 27-DEC-23 1TL2 1 HETSYN REVDAT 4 29-JUL-20 1TL2 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 SITE ATOM REVDAT 3 04-OCT-17 1TL2 1 REMARK REVDAT 2 24-FEB-09 1TL2 1 VERSN 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 INNATE IMMUNITY JRNL TITL 3 HOST DEFENSE OF THE JAPANESE HORSESHOE CRAB TACHYPLEUS JRNL TITL 4 TRIDENTATUS. JRNL REF EMBO J. V. 18 2313 1999 JRNL REFN ISSN 0261-4189 JRNL PMID 10228146 JRNL DOI 10.1093/EMBOJ/18.9.2313 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 20892 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2072 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1905 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.009 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.025 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TL2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-98. REMARK 100 THE DEPOSITION ID IS D_1000000279. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 289.0 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20896 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 15.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SHARP, CCP4, SHELXL-97 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.54000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 49.08000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 49.08000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.54000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 VAL A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 96 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 PHE A 236 CA - C - O ANGL. DEV. = -14.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LEU A 93 11.34 REMARK 500 ASP A 118 10.72 REMARK 500 REMARK 500 REMARK: NULL DBREF 1TL2 A 1 236 UNP Q27084 TAL2_TACTR 20 255 SEQADV 1TL2 VAL A 129 UNP Q27084 ILE 148 CONFLICT SEQADV 1TL2 TYR A 213 UNP Q27084 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 NDG A 237 15 HET NDG A 238 15 HET NDG A 239 15 HET NDG A 240 15 HET NDG A 241 15 HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETSYN NDG N-ACETYL-ALPHA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NDG ALPHA-D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2- HETSYN 3 NDG ACETAMIDO-2-DEOXY-GLUCOSE; 2-(ACETYLAMINO)-2-DEOXY-A- HETSYN 4 NDG D-GLUCOPYRANOSE FORMUL 2 NDG 5(C8 H15 N O6) FORMUL 7 HOH *158(H2 O) 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