HEADER SUGAR BINDING PROTEIN 16-OCT-14 4RL7 TITLE CRYSTAL STRUCTURE OF HUMAN GALECTIN-3 CRD IN COMPLEX WITH LACTOSE (PH TITLE 2 7.5, PEG6000) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 111-250; COMPND 5 SYNONYM: GAL-3, 35 KDA LECTIN, CARBOHYDRATE-BINDING PROTEIN 35, CBP COMPND 6 35, GALACTOSE-SPECIFIC LECTIN 3, GALACTOSIDE-BINDING PROTEIN, GALBP, COMPND 7 IGE-BINDING PROTEIN, L-31, LAMININ-BINDING PROTEIN, LECTIN L-29, MAC- COMPND 8 2 ANTIGEN; COMPND 9 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: LGALS3, MAC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.SU REVDAT 4 08-NOV-23 4RL7 1 REMARK REVDAT 3 24-AUG-22 4RL7 1 JRNL HETSYN REVDAT 2 29-JUL-20 4RL7 1 COMPND REMARK SEQADV HET REVDAT 2 2 1 HETNAM FORMUL LINK SITE REVDAT 2 3 1 ATOM REVDAT 1 11-MAR-15 4RL7 0 JRNL AUTH J.SU,T.ZHANG,P.WANG,F.LIU,G.TAI,Y.ZHOU JRNL TITL THE WATER NETWORK IN GALECTIN-3 LIGAND BINDING SITE GUIDES JRNL TITL 2 INHIBITOR DESIGN. JRNL REF ACTA BIOCHIM.BIOPHYS.SIN. V. 47 192 2015 JRNL REFN ESSN 1745-7270 JRNL PMID 25662390 JRNL DOI 10.1093/ABBS/GMU132 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 8824 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 886 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 23.7647 - 3.6308 0.94 1405 156 0.1400 0.1996 REMARK 3 2 3.6308 - 2.8835 0.94 1341 153 0.1467 0.2448 REMARK 3 3 2.8835 - 2.5194 0.94 1313 142 0.1857 0.2494 REMARK 3 4 2.5194 - 2.2893 0.95 1318 146 0.1842 0.2673 REMARK 3 5 2.2893 - 2.1253 0.94 1281 144 0.1894 0.2836 REMARK 3 6 2.1253 - 2.0000 0.93 1280 145 0.2001 0.2869 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.790 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 : 0.008 1170 REMARK 3 ANGLE : 1.261 1592 REMARK 3 CHIRALITY : 0.049 176 REMARK 3 PLANARITY : 0.006 204 REMARK 3 DIHEDRAL : 19.206 483 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: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I/F_MINUS AND I/F_PLUS COLUMNS. REMARK 4 REMARK 4 4RL7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000087484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 297 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7107 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8861 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 27.583 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 4R9D REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 18.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.50000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.50000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.90000 REMARK 290 SMTRY3 4 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 107 REMARK 465 SER A 108 REMARK 465 HIS A 109 REMARK 465 MET A 110 REMARK 465 ALA A 111 REMARK 465 GLY A 112 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N ILE A 231 O HOH A 435 2.02 REMARK 500 OD2 ASP A 241 O HOH A 491 2.05 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 LEU A 218 -61.27 -108.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R9A RELATED DB: PDB REMARK 900 RELATED ID: 4R9B RELATED DB: PDB REMARK 900 RELATED ID: 4R9C RELATED DB: PDB REMARK 900 RELATED ID: 4R9D RELATED DB: PDB DBREF 4RL7 A 111 250 UNP P17931 LEG3_HUMAN 111 250 SEQADV 4RL7 GLY A 107 UNP P17931 EXPRESSION TAG SEQADV 4RL7 SER A 108 UNP P17931 EXPRESSION TAG SEQADV 4RL7 HIS A 109 UNP P17931 EXPRESSION TAG SEQADV 4RL7 MET A 110 UNP P17931 EXPRESSION TAG SEQRES 1 A 144 GLY SER HIS MET ALA GLY PRO LEU ILE VAL PRO TYR ASN SEQRES 2 A 144 LEU PRO LEU PRO GLY GLY VAL VAL PRO ARG MET LEU ILE SEQRES 3 A 144 THR ILE LEU GLY THR VAL LYS PRO ASN ALA ASN ARG ILE SEQRES 4 A 144 ALA LEU ASP PHE GLN ARG GLY ASN ASP VAL ALA PHE HIS SEQRES 5 A 144 PHE ASN PRO ARG PHE ASN GLU ASN ASN ARG ARG VAL ILE SEQRES 6 A 144 VAL CYS ASN THR LYS LEU ASP ASN ASN TRP GLY ARG GLU SEQRES 7 A 144 GLU ARG GLN SER VAL PHE PRO PHE GLU SER GLY LYS PRO SEQRES 8 A 144 PHE LYS ILE GLN VAL LEU VAL GLU PRO ASP HIS PHE LYS SEQRES 9 A 144 VAL ALA VAL ASN ASP ALA HIS LEU LEU GLN TYR ASN HIS SEQRES 10 A 144 ARG VAL LYS LYS LEU ASN GLU ILE SER LYS LEU GLY ILE SEQRES 11 A 144 SER GLY ASP ILE ASP LEU THR SER ALA SER TYR THR MET SEQRES 12 A 144 ILE HET BGC B 1 12 HET GAL B 2 11 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 2 BGC C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 3 HOH *94(H2 O) HELIX 1 1 LYS A 227 ILE A 231 5 5 SHEET 1 A 6 TYR A 118 PRO A 121 0 SHEET 2 A 6 LYS A 233 GLY A 238 -1 O ILE A 236 N TYR A 118 SHEET 3 A 6 ILE A 145 ARG A 151 -1 N ASP A 148 O GLY A 235 SHEET 4 A 6 ASP A 154 GLU A 165 -1 O PHE A 159 N LEU A 147 SHEET 5 A 6 ARG A 168 LEU A 177 -1 O VAL A 170 N ARG A 162 SHEET 6 A 6 ASN A 180 TRP A 181 -1 O ASN A 180 N LEU A 177 SHEET 1 B 6 TYR A 118 PRO A 121 0 SHEET 2 B 6 LYS A 233 GLY A 238 -1 O ILE A 236 N TYR A 118 SHEET 3 B 6 ILE A 145 ARG A 151 -1 N ASP A 148 O GLY A 235 SHEET 4 B 6 ASP A 154 GLU A 165 -1 O PHE A 159 N LEU A 147 SHEET 5 B 6 ARG A 168 LEU A 177 -1 O VAL A 170 N ARG A 162 SHEET 6 B 6 GLU A 185 GLN A 187 -1 O GLU A 185 N CYS A 173 SHEET 1 C 5 ALA A 216 ASN A 222 0 SHEET 2 C 5 HIS A 208 VAL A 213 -1 N VAL A 211 O LEU A 218 SHEET 3 C 5 PRO A 197 VAL A 204 -1 N LEU A 203 O LYS A 210 SHEET 4 C 5 MET A 130 VAL A 138 -1 N GLY A 136 O PHE A 198 SHEET 5 C 5 ILE A 240 MET A 249 -1 O SER A 244 N LEU A 135 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.41 CISPEP 1 VAL A 116 PRO A 117 0 5.31 CRYST1 36.200 57.800 63.000 90.00 90.00 90.00 P 21 21 21 4 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 0.027624 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015873 0.00000