HEADER SUGAR BINDING PROTEIN 22-APR-19 6RHL TITLE ROOM TEMPERATURE DATA OF GALECTIN-3C IN COMPLEX WITH A PAIR OF TITLE 2 ENANTIOMERIC LIGANDS: R ENANTIOMER 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS LECTIN, CARBOHYDRATE-BINDING PROTEIN, GALACTOSE-SPECIFIC LECTIN 3, KEYWDS 2 GALACTOSIDE-BINDING PROTEIN, GALBP, IGE-6 BINDING PROTEIN, L-31, KEYWDS 3 LAMININ-BINDING PROTEIN, LECTIN L-29, MAC-2, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.KUMAR,M.L.VERTERAMO,U.J.NILSSON,D.T.LOGAN REVDAT 3 24-JAN-24 6RHL 1 REMARK REVDAT 2 28-AUG-19 6RHL 1 JRNL REVDAT 1 21-AUG-19 6RHL 0 JRNL AUTH O.CALDARARU,R.KUMAR,E.OKSANEN,D.T.LOGAN,U.RYDE JRNL TITL ARE CRYSTALLOGRAPHIC B-FACTORS SUITABLE FOR CALCULATING JRNL TITL 2 PROTEIN CONFORMATIONAL ENTROPY? JRNL REF PHYS CHEM CHEM PHYS V. 21 18149 2019 JRNL REFN ESSN 1463-9084 JRNL PMID 31389436 JRNL DOI 10.1039/C9CP02504A REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 34936 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1697 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 29.2089 - 2.9738 1.00 2956 160 0.1422 0.1632 REMARK 3 2 2.9738 - 2.3607 1.00 2814 152 0.1411 0.1602 REMARK 3 3 2.3607 - 2.0624 1.00 2801 132 0.1077 0.1612 REMARK 3 4 2.0624 - 1.8739 1.00 2801 119 0.0944 0.1434 REMARK 3 5 1.8739 - 1.7396 1.00 2764 147 0.1011 0.1561 REMARK 3 6 1.7396 - 1.6370 1.00 2767 126 0.1093 0.1472 REMARK 3 7 1.6370 - 1.5551 1.00 2756 144 0.1317 0.1793 REMARK 3 8 1.5551 - 1.4874 1.00 2728 135 0.1606 0.2308 REMARK 3 9 1.4874 - 1.4301 1.00 2731 158 0.1888 0.2458 REMARK 3 10 1.4301 - 1.3808 1.00 2747 134 0.2262 0.2339 REMARK 3 11 1.3808 - 1.3376 1.00 2725 147 0.2737 0.2768 REMARK 3 12 1.3376 - 1.2994 0.98 2649 143 0.3050 0.3101 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.960 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 : 0.015 1219 REMARK 3 ANGLE : 1.224 1666 REMARK 3 CHIRALITY : 0.107 184 REMARK 3 PLANARITY : 0.008 218 REMARK 3 DIHEDRAL : 14.803 456 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 6RHL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.652 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34990 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 29.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 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: PHENIX REMARK 200 STARTING MODEL: 3ZSL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 0.1 M TRIS/HCL PH 7.5, REMARK 280 0.4 M NASCN, 7.9 MM BETA-MERCAPTOETHANOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 18.59100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.96800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.20150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.96800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.59100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.20150 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO A 113 CG CD REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 183 CD 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 0.08 89.80 REMARK 500 ASN A 141 54.47 -114.14 REMARK 500 ASN A 164 81.31 -154.59 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 J0T A 301 DBREF 6RHL 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 J0T A 301 65 HETNAM J0T (2~{S},3~{R},4~{S},5~{R},6~{R})-4-[4-(3-FLUOROPHENYL)- HETNAM 2 J0T 1,2,3-TRIAZOL-1-YL]-2-[(2~{R})-3-[4-(3-FLUOROPHENYL)- HETNAM 3 J0T 1,2,3-TRIAZOL-1-YL]-2-OXIDANYL-PROPYL]SULFANYL-6- HETNAM 4 J0T (HYDROXYMETHYL)OXANE-3,5-DIOL FORMUL 2 J0T C25 H26 F2 N6 O5 S FORMUL 3 HOH *97(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 ILE A 236 N TYR A 118 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 ILE A 236 N TYR A 118 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 219 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 ILE A 134 O ILE A 200 SHEET 5 AA3 5 ILE A 240 MET A 249 -1 O THR A 248 N LEU A 131 CISPEP 1 VAL A 116 PRO A 117 0 0.45 SITE 1 AC1 11 ARG A 144 ILE A 145 ALA A 146 HIS A 158 SITE 2 AC1 11 ASN A 160 ARG A 162 ASN A 174 GLU A 184 SITE 3 AC1 11 ARG A 186 SER A 237 HOH A 423 CRYST1 37.182 58.403 63.936 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 0.026895 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017122 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015641 0.00000