HEADER SUGAR BINDING PROTEIN 10-SEP-19 6KXA TITLE GALECTIN-3 CRD BINDS TO GALA DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GAL-3,35 KDA LECTIN,CARBOHYDRATE-BINDING PROTEIN 35,CBP 35, COMPND 5 GALACTOSE-SPECIFIC LECTIN 3,GALACTOSIDE-BINDING PROTEIN,GALBP,IGE- COMPND 6 BINDING PROTEIN,L-31,LAMININ-BINDING PROTEIN,LECTIN L-29,MAC-2 COMPND 7 ANTIGEN; COMPND 8 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 GALECTIN-3 CRD BINDS TO GALA DIMER, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SU REVDAT 4 27-MAR-24 6KXA 1 REMARK REVDAT 3 21-APR-21 6KXA 1 JRNL REVDAT 2 30-SEP-20 6KXA 1 JRNL REVDAT 1 26-AUG-20 6KXA 0 JRNL AUTH Y.ZHENG,J.SU,M.C.MILLER,J.GENG,X.XU,T.ZHANG,M.MAYZEL,Y.ZHOU, JRNL AUTH 2 K.H.MAYO,G.TAI JRNL TITL TOPSY-TURVY BINDING OF NEGATIVELY CHARGED HOMOGALACTURONAN JRNL TITL 2 OLIGOSACCHARIDES TO GALECTIN-3. JRNL REF GLYCOBIOLOGY V. 31 341 2021 JRNL REFN ESSN 1460-2423 JRNL PMID 32909036 JRNL DOI 10.1093/GLYCOB/CWAA080 REMARK 2 REMARK 2 RESOLUTION. 1.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 37651 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.330 REMARK 3 FREE R VALUE TEST SET COUNT : 2008 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 19.4030 - 2.9613 1.00 2717 152 0.1482 0.1496 REMARK 3 2 2.9613 - 2.3517 1.00 2609 146 0.1521 0.1685 REMARK 3 3 2.3517 - 2.0548 0.99 2556 148 0.1469 0.1527 REMARK 3 4 2.0548 - 1.8671 1.00 2545 142 0.1440 0.1967 REMARK 3 5 1.8671 - 1.7334 1.00 2551 140 0.1577 0.1742 REMARK 3 6 1.7334 - 1.6313 1.00 2536 142 0.1661 0.1966 REMARK 3 7 1.6313 - 1.5496 1.00 2536 147 0.1569 0.1902 REMARK 3 8 1.5496 - 1.4822 1.00 2533 141 0.1662 0.2012 REMARK 3 9 1.4822 - 1.4251 1.00 2529 146 0.1801 0.2056 REMARK 3 10 1.4251 - 1.3760 1.00 2521 131 0.2074 0.2532 REMARK 3 11 1.3760 - 1.3329 1.00 2508 146 0.2540 0.2642 REMARK 3 12 1.3329 - 1.2949 1.00 2505 148 0.2817 0.3090 REMARK 3 13 1.2949 - 1.2608 1.00 2505 135 0.3181 0.2949 REMARK 3 14 1.2608 - 1.2300 0.99 2492 144 0.4570 0.4974 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 21.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.61 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 1177 REMARK 3 ANGLE : 1.011 1603 REMARK 3 CHIRALITY : 0.091 177 REMARK 3 PLANARITY : 0.008 207 REMARK 3 DIHEDRAL : 27.441 490 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 6KXA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013802. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-19 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37730 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 REMARK 200 RESOLUTION RANGE LOW (A) : 19.403 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.62800 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 (%): 39.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 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 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 17.93800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.93350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.63800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.93350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.93800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.63800 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 TOTAL BURIED SURFACE AREA: 580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL 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 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 ARG A 129 2.79 81.17 REMARK 500 ASN A 164 72.73 -157.12 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 637 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 638 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A 639 DISTANCE = 6.53 ANGSTROMS DBREF 6KXA A 113 250 UNP P17931 LEG3_HUMAN 113 250 SEQRES 1 A 138 PRO LEU ILE VAL PRO TYR ASN LEU PRO LEU PRO GLY GLY SEQRES 2 A 138 VAL VAL PRO ARG MET LEU ILE THR ILE LEU GLY THR VAL SEQRES 3 A 138 LYS PRO ASN ALA ASN ARG ILE ALA LEU ASP PHE GLN ARG SEQRES 4 A 138 GLY ASN ASP VAL ALA PHE HIS PHE ASN PRO ARG PHE ASN SEQRES 5 A 138 GLU ASN ASN ARG ARG VAL ILE VAL CYS ASN THR LYS LEU SEQRES 6 A 138 ASP ASN ASN TRP GLY ARG GLU GLU ARG GLN SER VAL PHE SEQRES 7 A 138 PRO PHE GLU SER GLY LYS PRO PHE LYS ILE GLN VAL LEU SEQRES 8 A 138 VAL GLU PRO ASP HIS PHE LYS VAL ALA VAL ASN ASP ALA SEQRES 9 A 138 HIS LEU LEU GLN TYR ASN HIS ARG VAL LYS LYS LEU ASN SEQRES 10 A 138 GLU ILE SER LYS LEU GLY ILE SER GLY ASP ILE ASP LEU SEQRES 11 A 138 THR SER ALA SER TYR THR MET ILE HET GTR B 1 13 HET ADA B 2 12 HETNAM GTR BETA-D-GALACTOPYRANURONIC ACID HETNAM ADA ALPHA-D-GALACTOPYRANURONIC ACID HETSYN GTR BETA-D-GALACTURONIC ACID; D-GALACTURONIC ACID; HETSYN 2 GTR GALACTURONIC ACID HETSYN ADA ALPHA-D-GALACTURONIC ACID; D-GALACTURONIC ACID; HETSYN 2 ADA GALACTURONIC ACID; ALPHA D-GALACTURONIC ACID FORMUL 2 GTR C6 H10 O7 FORMUL 2 ADA C6 H10 O7 FORMUL 3 HOH *239(H2 O) HELIX 1 AA1 LYS A 227 ILE A 231 5 5 SHEET 1 AA1 6 TYR A 118 PRO A 121 0 SHEET 2 AA1 6 LYS A 233 GLY A 238 -1 O LEU A 234 N LEU A 120 SHEET 3 AA1 6 ILE A 145 ARG A 151 -1 N GLN A 150 O LYS A 233 SHEET 4 AA1 6 ASP A 154 GLU A 165 -1 O PHE A 157 N PHE A 149 SHEET 5 AA1 6 ARG A 168 LEU A 177 -1 O VAL A 170 N ARG A 162 SHEET 6 AA1 6 ASN A 180 TRP A 181 -1 O ASN A 180 N LEU A 177 SHEET 1 AA2 6 TYR A 118 PRO A 121 0 SHEET 2 AA2 6 LYS A 233 GLY A 238 -1 O LEU A 234 N LEU A 120 SHEET 3 AA2 6 ILE A 145 ARG A 151 -1 N GLN A 150 O LYS A 233 SHEET 4 AA2 6 ASP A 154 GLU A 165 -1 O PHE A 157 N PHE A 149 SHEET 5 AA2 6 ARG A 168 LEU A 177 -1 O VAL A 170 N ARG A 162 SHEET 6 AA2 6 GLU A 185 GLN A 187 -1 O GLN A 187 N ILE A 171 SHEET 1 AA3 5 ALA A 216 ASN A 222 0 SHEET 2 AA3 5 HIS A 208 VAL A 213 -1 N VAL A 211 O LEU A 218 SHEET 3 AA3 5 PRO A 197 VAL A 204 -1 N LEU A 203 O LYS A 210 SHEET 4 AA3 5 MET A 130 VAL A 138 -1 N GLY A 136 O PHE A 198 SHEET 5 AA3 5 ILE A 240 MET A 249 -1 O THR A 248 N LEU A 131 LINK O4 GTR B 1 C1 ADA B 2 1555 1555 1.42 CISPEP 1 VAL A 116 PRO A 117 0 -1.42 CRYST1 35.876 57.276 61.867 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 0.027874 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016164 0.00000