HEADER SUGAR BINDING PROTEIN 03-SEP-20 7CYB TITLE SAIMIRI BOLIVIENSIS BOLIVIENSIS GALECTIN-13 WITH GLYCEROL COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GALECTIN-13; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SAIMIRI BOLIVIENSIS BOLIVIENSIS; SOURCE 3 ORGANISM_COMMON: BOLIVIAN SQUIRREL MONKEY; SOURCE 4 ORGANISM_TAXID: 39432; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SAIMIRI BOLIVIENSIS BOLIVIENSIS GALECTIN-13 WITH GLYCEROL, SUGAR KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SU REVDAT 3 29-NOV-23 7CYB 1 REMARK REVDAT 2 06-OCT-21 7CYB 1 JRNL REVDAT 1 16-JUN-21 7CYB 0 JRNL AUTH X.LI,Y.YAO,T.LIU,K.GU,Q.HAN,W.ZHANG,G.J.AYALA,Y.LIU,H.NA, JRNL AUTH 2 J.YU,F.ZHANG,K.H.MAYO,J.SU JRNL TITL ACTIN BINDING TO GALECTIN-13/PLACENTAL PROTEIN-13 OCCURS JRNL TITL 2 INDEPENDENTLY OF THE GALECTIN CANONICAL LIGAND-BINDING SITE. JRNL REF GLYCOBIOLOGY V. 31 1219 2021 JRNL REFN ESSN 1460-2423 JRNL PMID 34080003 JRNL DOI 10.1093/GLYCOB/CWAB047 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 18943 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1900 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.8200 - 3.8500 0.98 1240 138 0.1589 0.1769 REMARK 3 2 3.8500 - 3.0600 0.99 1221 140 0.1488 0.1647 REMARK 3 3 3.0600 - 2.6700 0.98 1221 134 0.1614 0.1971 REMARK 3 4 2.6700 - 2.4300 0.99 1223 137 0.1540 0.1789 REMARK 3 5 2.4300 - 2.2500 0.99 1226 127 0.1462 0.1939 REMARK 3 6 2.2500 - 2.1200 0.97 1195 136 0.1451 0.1880 REMARK 3 7 2.1200 - 2.0200 0.98 1217 133 0.1565 0.1669 REMARK 3 8 2.0200 - 1.9300 0.99 1224 137 0.1495 0.1839 REMARK 3 9 1.9300 - 1.8500 0.99 1190 139 0.1529 0.1983 REMARK 3 10 1.8500 - 1.7900 0.99 1238 135 0.1540 0.2012 REMARK 3 11 1.7900 - 1.7300 0.99 1206 139 0.1552 0.1969 REMARK 3 12 1.7300 - 1.6800 0.99 1220 135 0.1568 0.1993 REMARK 3 13 1.6800 - 1.6400 0.99 1213 141 0.1585 0.1957 REMARK 3 14 1.6400 - 1.6000 0.98 1209 129 0.1688 0.2361 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.32 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7CYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018442. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18965 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.09900 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 6KJX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.45650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 63 -58.12 -125.27 REMARK 500 LYS A 76 -144.51 -95.37 REMARK 500 TYR A 113 147.58 -171.27 REMARK 500 ARG A 131 -143.66 86.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 DBREF1 7CYB A 4 142 UNP A0A2K6TQH4_SAIBB DBREF2 7CYB A A0A2K6TQH4 1 139 SEQADV 7CYB GLY A 1 UNP A0A2K6TQH EXPRESSION TAG SEQADV 7CYB SER A 2 UNP A0A2K6TQH EXPRESSION TAG SEQADV 7CYB HIS A 3 UNP A0A2K6TQH EXPRESSION TAG SEQRES 1 A 142 GLY SER HIS MET SER SER LEU PRO VAL PRO TYR LYS LEU SEQRES 2 A 142 PRO VAL SER LEU SER THR GLY ALA CYS VAL ILE ILE LYS SEQRES 3 A 142 GLY ARG PRO LYS LEU SER PHE ILE ASN ASP PRO GLN LEU SEQRES 4 A 142 GLN VAL ASP PHE TYR THR GLY THR ASP GLU ASP SER ASP SEQRES 5 A 142 ILE ALA PHE HIS PHE ARG VAL HIS PHE GLY HIS ARG VAL SEQRES 6 A 142 VAL MET ASN SER LEU GLU PHE GLY VAL TRP LYS LEU GLU SEQRES 7 A 142 GLU LYS ILE HIS TYR VAL PRO PHE GLU ASP GLY GLU PRO SEQRES 8 A 142 PHE GLU LEU ARG ILE TYR VAL ARG HIS SER GLU TYR GLU SEQRES 9 A 142 VAL LYS VAL ASN GLY GLN TYR ILE TYR GLY PHE ALA HIS SEQRES 10 A 142 ARG HIS PRO PRO SER TYR VAL LYS MET ILE GLN VAL TRP SEQRES 11 A 142 ARG ASP VAL SER LEU THR SER VAL CYS VAL TYR ASN HET GOL A 201 14 HET GOL A 202 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *168(H2 O) HELIX 1 AA1 SER A 32 ASP A 36 5 5 HELIX 2 AA2 PRO A 120 VAL A 124 5 5 SHEET 1 AA1 6 TYR A 11 PRO A 14 0 SHEET 2 AA1 6 MET A 126 ARG A 131 -1 O VAL A 129 N TYR A 11 SHEET 3 AA1 6 GLN A 38 TYR A 44 -1 N GLN A 40 O TRP A 130 SHEET 4 AA1 6 ILE A 53 HIS A 60 -1 O VAL A 59 N LEU A 39 SHEET 5 AA1 6 ARG A 64 GLU A 71 -1 O VAL A 66 N ARG A 58 SHEET 6 AA1 6 VAL A 74 TRP A 75 -1 O VAL A 74 N GLU A 71 SHEET 1 AA2 6 TYR A 11 PRO A 14 0 SHEET 2 AA2 6 MET A 126 ARG A 131 -1 O VAL A 129 N TYR A 11 SHEET 3 AA2 6 GLN A 38 TYR A 44 -1 N GLN A 40 O TRP A 130 SHEET 4 AA2 6 ILE A 53 HIS A 60 -1 O VAL A 59 N LEU A 39 SHEET 5 AA2 6 ARG A 64 GLU A 71 -1 O VAL A 66 N ARG A 58 SHEET 6 AA2 6 GLU A 79 ILE A 81 -1 O GLU A 79 N MET A 67 SHEET 1 AA3 5 GLN A 110 ALA A 116 0 SHEET 2 AA3 5 GLU A 102 VAL A 107 -1 N VAL A 105 O TYR A 113 SHEET 3 AA3 5 PHE A 92 VAL A 98 -1 N TYR A 97 O GLU A 104 SHEET 4 AA3 5 CYS A 22 PRO A 29 -1 N ILE A 25 O LEU A 94 SHEET 5 AA3 5 VAL A 133 TYR A 141 -1 O CYS A 139 N ILE A 24 CISPEP 1 VAL A 9 PRO A 10 0 0.07 SITE 1 AC1 6 HIS A 56 ARG A 58 ASN A 68 GLU A 78 SITE 2 AC1 6 HOH A 358 HOH A 381 SITE 1 AC2 9 PHE A 61 GLY A 62 HIS A 63 ARG A 64 SITE 2 AC2 9 VAL A 65 HIS A 82 TYR A 83 VAL A 84 SITE 3 AC2 9 HOH A 326 CRYST1 33.407 58.913 40.701 90.00 113.34 90.00 P 1 21 1 2 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 0.029934 0.000000 0.012918 0.00000 SCALE2 0.000000 0.016974 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026760 0.00000