HEADER SUGAR BINDING PROTEIN 20-FEB-20 6Y4C TITLE STRUCTURE OF GALECTIN-3C IN COMPLEX WITH LACTOSE DETERMINED BY SERIAL TITLE 2 CRYSTALLOGRAPHY USING AN XTALTOOL SUPPORT 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, SYNCHROTRON SERIAL CRYSTALLOGRAPHY, SOLID SUPPORT, KEYWDS 2 XTALTOOL, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SHILOVA,M.HAKANSSON,M.WELIN,R.KOVACIC,U.MUELLER,D.T.LOGAN REVDAT 4 24-JAN-24 6Y4C 1 REMARK REVDAT 3 16-SEP-20 6Y4C 1 JRNL HETSYN REVDAT 2 29-JUL-20 6Y4C 1 COMPND REMARK HET HETNAM REVDAT 2 2 1 FORMUL LINK SITE ATOM REVDAT 1 17-JUN-20 6Y4C 0 JRNL AUTH A.SHILOVA,H.LEBRETTE,O.AURELIUS,J.NAN,M.WELIN,R.KOVACIC, JRNL AUTH 2 S.GHOSH,C.SAFARI,R.J.FRIEL,M.MILAS,Z.MATEJ,M.HOGBOM, JRNL AUTH 3 G.BRANDEN,M.KLOOS,R.L.SHOEMAN,B.DOAK,T.URSBY,M.HAKANSSON, JRNL AUTH 4 D.T.LOGAN,U.MUELLER JRNL TITL CURRENT STATUS AND FUTURE OPPORTUNITIES FOR SERIAL JRNL TITL 2 CRYSTALLOGRAPHY AT MAX IV LABORATORY. JRNL REF J.SYNCHROTRON RADIAT. V. 27 1095 2020 JRNL REFN ESSN 1600-5775 JRNL PMID 32876583 JRNL DOI 10.1107/S1600577520008735 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3845 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 15137 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1525 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 42.9100 - 3.7800 1.00 1369 153 0.1416 0.1483 REMARK 3 2 3.7800 - 3.0000 1.00 1305 145 0.1415 0.1650 REMARK 3 3 3.0000 - 2.6200 1.00 1262 140 0.1464 0.1878 REMARK 3 4 2.6200 - 2.3800 0.99 1280 144 0.1413 0.2044 REMARK 3 5 2.3800 - 2.2100 0.99 1244 137 0.1370 0.1960 REMARK 3 6 2.2100 - 2.0800 0.99 1237 138 0.1312 0.1829 REMARK 3 7 2.0800 - 1.9800 0.98 1237 138 0.1395 0.1925 REMARK 3 8 1.9800 - 1.8900 0.97 1215 135 0.1407 0.1948 REMARK 3 9 1.8900 - 1.8200 0.96 1182 137 0.1603 0.2181 REMARK 3 10 1.8200 - 1.7500 0.94 1173 134 0.1838 0.2349 REMARK 3 11 1.7500 - 1.7000 0.90 1108 124 0.2095 0.2602 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) : 0.153 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.184 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.10 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 1187 REMARK 3 ANGLE : 0.877 1623 REMARK 3 CHIRALITY : 0.061 188 REMARK 3 PLANARITY : 0.006 210 REMARK 3 DIHEDRAL : 13.763 463 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 13.2007 0.8047 6.4395 REMARK 3 T TENSOR REMARK 3 T11: 0.0933 T22: 0.1006 REMARK 3 T33: 0.1006 T12: 0.0011 REMARK 3 T13: -0.0118 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.0544 L22: 1.8648 REMARK 3 L33: 2.2742 L12: 0.1357 REMARK 3 L13: -0.3376 L23: -1.1489 REMARK 3 S TENSOR REMARK 3 S11: 0.0206 S12: -0.0036 S13: -0.0536 REMARK 3 S21: -0.0483 S22: -0.0045 S23: 0.0047 REMARK 3 S31: 0.1240 S32: 0.0643 S33: -0.0182 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 6Y4C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292105480. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 15555 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) : 0.9800 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15552 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 139.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 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 : 2.500 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: 6EYM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN ON AN XTALTOOL REMARK 280 SUPPORT (JENA BIOSCIENCE) OVER A 24 WELL VDX-PLATE WITH 1 ML REMARK 280 RESERVOIR. THE DROP CONSISTED OF 1 MICROLITRE 20 MG/ML PROTEIN REMARK 280 IN 10 MM SODIUM PHOSPHATE PH 7.4, 100 MM NACL, 10 MM BETA- REMARK 280 MERCAPTOETHANOL, 2 MM LACTOSE), 0.25 MICROLITRE OF SEED CRYSTALS REMARK 280 IN A STABILIZATION SOLUTION CONTAINING 0.1 M TRIS PH 7.5, 33% (W/ REMARK 280 V) PEG 4000, 0.1 M MGCL2, 0.2 M NASCN) AND 0.75 MICROLITRE REMARK 280 RESERVOIR SOLUTION CONTAINING 0.1 M TRIS PH 7.5, 30% PEG 4000, REMARK 280 0.05 M MGCL2, 0.2 M NASCN AND 8 MM BETA-MERCAPTOETHANOL., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 18.33000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.86000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.02500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.86000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.33000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.02500 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: 510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 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 N CA CB CG 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 -1.21 85.92 REMARK 500 ASN A 164 81.52 -151.94 REMARK 500 REMARK 500 REMARK: NULL DBREF 6Y4C 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 BGC B 1 12 HET GAL B 2 11 HET CL A 502 1 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM CL CHLORIDE ION 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 CL CL 1- FORMUL 4 HOH *104(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 GLU A 185 N CYS A 173 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 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.40 CISPEP 1 VAL A 116 PRO A 117 0 -0.89 CRYST1 36.660 58.050 63.720 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 0.027278 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017227 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015694 0.00000