HEADER SUGAR BINDING PROTEIN 17-MAR-22 7XAC TITLE DIMERIC STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH TWO GLYCEROL COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN-7; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GAL-7,HKL-14,PI7,P53-INDUCED GENE 1 PROTEIN; COMPND 5 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: LGALS7, PIG1, LGALS7B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SUGAR BINDING PROTEIN, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR Y.L.SI REVDAT 2 29-NOV-23 7XAC 1 REMARK REVDAT 1 11-JAN-23 7XAC 0 JRNL AUTH Y.LIANG,Y.WANG,X.ZHU,J.CAI,A.SHI,J.HUANG,Q.ZHU,Y.SI JRNL TITL BINDING OF GLYCEROL TO HUMAN GALECTIN-7 EXPANDS STABILITY JRNL TITL 2 AND MODULATES ITS FUNCTIONS. JRNL REF INT J MOL SCI V. 23 2022 JRNL REFN ESSN 1422-0067 JRNL PMID 36293173 JRNL DOI 10.3390/IJMS232012318 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 23570 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.490 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 19.8500 - 4.3300 1.00 1660 154 0.1872 0.2191 REMARK 3 2 4.3200 - 3.4400 1.00 1577 146 0.1620 0.2134 REMARK 3 3 3.4400 - 3.0100 1.00 1561 145 0.1880 0.2483 REMARK 3 4 3.0100 - 2.7300 1.00 1555 144 0.2146 0.2574 REMARK 3 5 2.7300 - 2.5400 1.00 1541 144 0.2254 0.3030 REMARK 3 6 2.5400 - 2.3900 1.00 1537 142 0.2190 0.2768 REMARK 3 7 2.3900 - 2.2700 1.00 1544 142 0.2116 0.2731 REMARK 3 8 2.2700 - 2.1700 0.99 1499 140 0.2058 0.2821 REMARK 3 9 2.1700 - 2.0900 1.00 1526 141 0.2078 0.2621 REMARK 3 10 2.0900 - 2.0100 1.00 1532 142 0.2075 0.2416 REMARK 3 11 2.0100 - 1.9500 1.00 1515 141 0.2215 0.2861 REMARK 3 12 1.9500 - 1.8900 0.98 1496 139 0.2202 0.2471 REMARK 3 13 1.8900 - 1.8500 1.00 1515 140 0.2194 0.2539 REMARK 3 14 1.8400 - 1.8000 0.99 1512 140 0.2254 0.2861 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.92 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7XAC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028391. 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) : 0.977 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23618 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.00100 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: MOLREP REMARK 200 STARTING MODEL: 1BKZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M MAGNESIUM CHLORIDE, REMARK 280 0.1M HEPES PH7.5, VAPOR DIFFUSION, 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 26.79800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.57950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.49200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.57950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.79800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.49200 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: DIMERIC 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 MET A 1 REMARK 465 MET B 1 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 O HOH A 312 O HOH A 385 2.18 REMARK 500 O HOH A 415 O HOH A 416 2.19 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 ASN A 3 154.90 177.24 REMARK 500 PRO A 80 39.37 -89.68 REMARK 500 ASN B 3 17.13 48.78 REMARK 500 PRO B 80 35.96 -85.41 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XAC A 1 136 UNP P47929 LEG7_HUMAN 1 136 DBREF 7XAC B 1 136 UNP P47929 LEG7_HUMAN 1 136 SEQRES 1 A 136 MET SER ASN VAL PRO HIS LYS SER SER LEU PRO GLU GLY SEQRES 2 A 136 ILE ARG PRO GLY THR VAL LEU ARG ILE ARG GLY LEU VAL SEQRES 3 A 136 PRO PRO ASN ALA SER ARG PHE HIS VAL ASN LEU LEU CYS SEQRES 4 A 136 GLY GLU GLU GLN GLY SER ASP ALA ALA LEU HIS PHE ASN SEQRES 5 A 136 PRO ARG LEU ASP THR SER GLU VAL VAL PHE ASN SER LYS SEQRES 6 A 136 GLU GLN GLY SER TRP GLY ARG GLU GLU ARG GLY PRO GLY SEQRES 7 A 136 VAL PRO PHE GLN ARG GLY GLN PRO PHE GLU VAL LEU ILE SEQRES 8 A 136 ILE ALA SER ASP ASP GLY PHE LYS ALA VAL VAL GLY ASP SEQRES 9 A 136 ALA GLN TYR HIS HIS PHE ARG HIS ARG LEU PRO LEU ALA SEQRES 10 A 136 ARG VAL ARG LEU VAL GLU VAL GLY GLY ASP VAL GLN LEU SEQRES 11 A 136 ASP SER VAL ARG ILE PHE SEQRES 1 B 136 MET SER ASN VAL PRO HIS LYS SER SER LEU PRO GLU GLY SEQRES 2 B 136 ILE ARG PRO GLY THR VAL LEU ARG ILE ARG GLY LEU VAL SEQRES 3 B 136 PRO PRO ASN ALA SER ARG PHE HIS VAL ASN LEU LEU CYS SEQRES 4 B 136 GLY GLU GLU GLN GLY SER ASP ALA ALA LEU HIS PHE ASN SEQRES 5 B 136 PRO ARG LEU ASP THR SER GLU VAL VAL PHE ASN SER LYS SEQRES 6 B 136 GLU GLN GLY SER TRP GLY ARG GLU GLU ARG GLY PRO GLY SEQRES 7 B 136 VAL PRO PHE GLN ARG GLY GLN PRO PHE GLU VAL LEU ILE SEQRES 8 B 136 ILE ALA SER ASP ASP GLY PHE LYS ALA VAL VAL GLY ASP SEQRES 9 B 136 ALA GLN TYR HIS HIS PHE ARG HIS ARG LEU PRO LEU ALA SEQRES 10 B 136 ARG VAL ARG LEU VAL GLU VAL GLY GLY ASP VAL GLN LEU SEQRES 11 B 136 ASP SER VAL ARG ILE PHE HET GOL A 201 6 HET GOL B 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *230(H2 O) HELIX 1 AA1 PRO A 115 VAL A 119 5 5 HELIX 2 AA2 PRO B 115 VAL B 119 5 5 SHEET 1 AA1 6 HIS A 6 SER A 9 0 SHEET 2 AA1 6 LEU A 121 GLY A 126 -1 O VAL A 124 N HIS A 6 SHEET 3 AA1 6 PHE A 33 LEU A 38 -1 N LEU A 38 O LEU A 121 SHEET 4 AA1 6 ALA A 47 ARG A 54 -1 O LEU A 49 N LEU A 37 SHEET 5 AA1 6 GLU A 59 GLU A 66 -1 O GLU A 59 N ARG A 54 SHEET 6 AA1 6 SER A 69 TRP A 70 -1 O SER A 69 N GLU A 66 SHEET 1 AA2 6 HIS A 6 SER A 9 0 SHEET 2 AA2 6 LEU A 121 GLY A 126 -1 O VAL A 124 N HIS A 6 SHEET 3 AA2 6 PHE A 33 LEU A 38 -1 N LEU A 38 O LEU A 121 SHEET 4 AA2 6 ALA A 47 ARG A 54 -1 O LEU A 49 N LEU A 37 SHEET 5 AA2 6 GLU A 59 GLU A 66 -1 O GLU A 59 N ARG A 54 SHEET 6 AA2 6 GLU A 74 ARG A 75 -1 O GLU A 74 N PHE A 62 SHEET 1 AA3 5 ALA A 105 ARG A 111 0 SHEET 2 AA3 5 GLY A 97 VAL A 102 -1 N ALA A 100 O TYR A 107 SHEET 3 AA3 5 GLN A 85 ALA A 93 -1 N ILE A 92 O LYS A 99 SHEET 4 AA3 5 THR A 18 VAL A 26 -1 N ILE A 22 O VAL A 89 SHEET 5 AA3 5 GLN A 129 PHE A 136 -1 O PHE A 136 N VAL A 19 SHEET 1 AA4 6 HIS B 6 SER B 9 0 SHEET 2 AA4 6 LEU B 121 GLY B 126 -1 O VAL B 124 N HIS B 6 SHEET 3 AA4 6 PHE B 33 LEU B 38 -1 N ASN B 36 O GLU B 123 SHEET 4 AA4 6 ALA B 47 ARG B 54 -1 O PHE B 51 N VAL B 35 SHEET 5 AA4 6 GLU B 59 GLU B 66 -1 O GLU B 59 N ARG B 54 SHEET 6 AA4 6 SER B 69 TRP B 70 -1 O SER B 69 N GLU B 66 SHEET 1 AA5 6 HIS B 6 SER B 9 0 SHEET 2 AA5 6 LEU B 121 GLY B 126 -1 O VAL B 124 N HIS B 6 SHEET 3 AA5 6 PHE B 33 LEU B 38 -1 N ASN B 36 O GLU B 123 SHEET 4 AA5 6 ALA B 47 ARG B 54 -1 O PHE B 51 N VAL B 35 SHEET 5 AA5 6 GLU B 59 GLU B 66 -1 O GLU B 59 N ARG B 54 SHEET 6 AA5 6 GLU B 74 ARG B 75 -1 O GLU B 74 N PHE B 62 SHEET 1 AA6 5 ALA B 105 ARG B 111 0 SHEET 2 AA6 5 GLY B 97 VAL B 102 -1 N ALA B 100 O TYR B 107 SHEET 3 AA6 5 PRO B 86 ALA B 93 -1 N LEU B 90 O VAL B 101 SHEET 4 AA6 5 VAL B 19 LEU B 25 -1 N ILE B 22 O VAL B 89 SHEET 5 AA6 5 GLN B 129 PHE B 136 -1 O PHE B 136 N VAL B 19 CRYST1 53.596 64.984 71.159 90.00 90.00 90.00 P 21 21 21 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 0.018658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014053 0.00000