HEADER SUGAR BINDING PROTEIN 29-NOV-22 8HL9 TITLE CRYSTAL STRUCTURE OF GALECTIN-8 C-CRD WITH PART OF LINKER COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GAL-8,PO66 CARBOHYDRATE-BINDING PROTEIN,PO66-CBP,PROSTATE COMPND 5 CARCINOMA TUMOR ANTIGEN 1,PCTA-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LGALS8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BINDING SUGAR, IMMUNOLOGICAL FUNCTION, LINKER, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.L.SI REVDAT 2 12-JUL-23 8HL9 1 JRNL REVDAT 1 05-JUL-23 8HL9 0 JRNL AUTH Y.SI,J.CAI,J.ZHU,Y.WANG,F.ZHANG,L.MENG,J.HUANG,A.SHI JRNL TITL LINKER REMODELS HUMAN GALECTIN-8 STRUCTURE AND REGULATES ITS JRNL TITL 2 HEMAGGLUTINATION AND PRO-APOPTOTIC ACTIVITY. JRNL REF INT.J.BIOL.MACROMOL. V. 245 25456 2023 JRNL REFN ISSN 0141-8130 JRNL PMID 37331541 JRNL DOI 10.1016/J.IJBIOMAC.2023.125456 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.0 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) : 19.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 24059 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.230 REMARK 3 FREE R VALUE TEST SET COUNT : 1979 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 19.6200 - 3.8500 0.99 1753 157 0.1897 0.2168 REMARK 3 2 3.8500 - 3.0600 0.99 1663 149 0.1816 0.2006 REMARK 3 3 3.0600 - 2.6700 1.00 1619 146 0.2096 0.2993 REMARK 3 4 2.6700 - 2.4300 1.00 1625 146 0.2151 0.2605 REMARK 3 5 2.4300 - 2.2500 0.99 1588 142 0.2079 0.2760 REMARK 3 6 2.2500 - 2.1200 0.87 1380 124 0.2578 0.2637 REMARK 3 7 2.1200 - 2.0200 1.00 1582 142 0.2124 0.2511 REMARK 3 8 2.0200 - 1.9300 0.92 1472 131 0.2984 0.3293 REMARK 3 9 1.9300 - 1.8500 0.97 1549 137 0.3126 0.3209 REMARK 3 10 1.8500 - 1.7900 1.00 1570 142 0.2404 0.2878 REMARK 3 11 1.7900 - 1.7300 1.00 1581 141 0.2172 0.2487 REMARK 3 12 1.7300 - 1.6800 1.00 1583 142 0.2231 0.3012 REMARK 3 13 1.6800 - 1.6400 1.00 1564 141 0.2248 0.2492 REMARK 3 14 1.6400 - 1.6000 1.00 1551 139 0.2259 0.2600 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 1161 REMARK 3 ANGLE : 0.910 1566 REMARK 3 CHIRALITY : 0.063 170 REMARK 3 PLANARITY : 0.010 203 REMARK 3 DIHEDRAL : 6.788 152 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 8HL9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300033839. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-21 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) : 0.987 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24410 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 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) : 0.52000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.0, 0.2M MGCL2, 30% REMARK 280 (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.37450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.45000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.68725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.45000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.45000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 95.06175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.45000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.45000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.68725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.45000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.45000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 95.06175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.37450 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 SER A 26 REMARK 465 GLY A 27 REMARK 465 THR A 28 REMARK 465 PRO A 29 REMARK 465 GLN A 30 REMARK 465 LEU A 31 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 334 O HOH A 338 6465 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 70 -72.32 -62.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 339 DISTANCE = 6.50 ANGSTROMS DBREF 8HL9 A 19 165 UNP O00214 LEG8_HUMAN 171 317 SEQRES 1 A 147 SER ARG GLU ASN VAL PRO LYS SER GLY THR PRO GLN LEU SEQRES 2 A 147 ARG LEU PRO PHE ALA ALA ARG LEU ASN THR PRO MET GLY SEQRES 3 A 147 PRO GLY ARG THR VAL VAL VAL LYS GLY GLU VAL ASN ALA SEQRES 4 A 147 ASN ALA LYS SER PHE ASN VAL ASP LEU LEU ALA GLY LYS SEQRES 5 A 147 SER LYS ASP ILE ALA LEU HIS LEU ASN PRO ARG LEU ASN SEQRES 6 A 147 ILE LYS ALA PHE VAL ARG ASN SER PHE LEU GLN GLU SER SEQRES 7 A 147 TRP GLY GLU GLU GLU ARG ASN ILE THR SER PHE PRO PHE SEQRES 8 A 147 SER PRO GLY MET TYR PHE GLU MET ILE ILE TYR CYS ASP SEQRES 9 A 147 VAL ARG GLU PHE LYS VAL ALA VAL ASN GLY VAL HIS SER SEQRES 10 A 147 LEU GLU TYR LYS HIS ARG PHE LYS GLU LEU SER SER ILE SEQRES 11 A 147 ASP THR LEU GLU ILE ASN GLY ASP ILE HIS LEU LEU GLU SEQRES 12 A 147 VAL ARG SER TRP FORMUL 2 HOH *139(H2 O) HELIX 1 AA1 GLU A 144 ILE A 148 5 5 SHEET 1 AA1 7 ASN A 22 PRO A 24 0 SHEET 2 AA1 7 PHE A 35 LEU A 39 -1 O ARG A 38 N VAL A 23 SHEET 3 AA1 7 THR A 150 GLY A 155 -1 O ILE A 153 N PHE A 35 SHEET 4 AA1 7 PHE A 62 LEU A 67 -1 N ASP A 65 O GLU A 152 SHEET 5 AA1 7 ILE A 74 ARG A 81 -1 O LEU A 78 N VAL A 64 SHEET 6 AA1 7 ALA A 86 LEU A 93 -1 O ALA A 86 N ARG A 81 SHEET 7 AA1 7 SER A 96 TRP A 97 -1 O SER A 96 N LEU A 93 SHEET 1 AA2 5 VAL A 133 LYS A 139 0 SHEET 2 AA2 5 GLU A 125 VAL A 130 -1 N VAL A 128 O SER A 135 SHEET 3 AA2 5 TYR A 114 CYS A 121 -1 N TYR A 120 O LYS A 127 SHEET 4 AA2 5 THR A 48 VAL A 55 -1 N VAL A 49 O ILE A 119 SHEET 5 AA2 5 ILE A 157 TRP A 165 -1 O HIS A 158 N GLU A 54 CISPEP 1 LEU A 33 PRO A 34 0 2.12 CRYST1 52.900 52.900 126.749 90.00 90.00 90.00 P 41 21 2 8 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 0.018904 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007890 0.00000