HEADER SUGAR BINDING PROTEIN 17-JAN-22 7TKW TITLE CRYSTAL STRUCTURE OF R14A HUMAN GALECTIN-7 MUTANT 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; COMPND 6 MUTATION: 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET22B KEYWDS HUMAN GALECTIN-7, DIMER INTERFACE MUTANT, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.T.H.PHAM,C.CALMETTES,N.DOUCET REVDAT 2 25-OCT-23 7TKW 1 REMARK REVDAT 1 25-JAN-23 7TKW 0 JRNL AUTH N.T.H.PHAM,C.CALMETTES,N.DOUCET JRNL TITL CRYSTAL STRUCTURE OF R14A HUMAN GALECTIN-7 MUTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 21590 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.370 REMARK 3 FREE R VALUE TEST SET COUNT : 1160 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 47.7400 - 3.7000 1.00 2689 157 0.1734 0.1982 REMARK 3 2 3.7000 - 2.9400 1.00 2602 142 0.1814 0.2431 REMARK 3 3 2.9400 - 2.5700 1.00 2569 139 0.2163 0.2591 REMARK 3 4 2.5700 - 2.3300 1.00 2517 149 0.2050 0.2309 REMARK 3 5 2.3300 - 2.1600 1.00 2536 146 0.1937 0.2239 REMARK 3 6 2.1600 - 2.0400 1.00 2521 146 0.2050 0.2579 REMARK 3 7 2.0400 - 1.9300 1.00 2507 131 0.2100 0.2350 REMARK 3 8 1.9300 - 1.8500 1.00 2489 150 0.2369 0.2852 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.53 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 2193 REMARK 3 ANGLE : 1.046 2968 REMARK 3 CHIRALITY : 0.296 311 REMARK 3 PLANARITY : 0.005 402 REMARK 3 DIHEDRAL : 22.973 833 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 7TKW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000262331. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97952 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21688 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 53.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.69200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 142.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : 0.88800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.80 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.12 REMARK 200 STARTING MODEL: 1BKZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M TRIS 8.0, REMARK 280 20 % W/V PEG 6000, PH 8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295.15K 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 26.87500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.20500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.47500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.20500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.87500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.47500 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 SER A 1 REMARK 465 ASN A 2 REMARK 465 SER B 1 REMARK 465 ASN B 2 REMARK 465 VAL B 3 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 GLN A 66 19.63 55.97 REMARK 500 PRO A 79 42.63 -82.29 REMARK 500 PRO B 79 38.42 -85.77 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 430 DISTANCE = 6.57 ANGSTROMS DBREF 7TKW A 1 135 UNP P47929 LEG7_HUMAN 2 136 DBREF 7TKW B 1 135 UNP P47929 LEG7_HUMAN 2 136 SEQADV 7TKW ALA A 14 UNP P47929 ARG 15 ENGINEERED MUTATION SEQADV 7TKW ALA B 14 UNP P47929 ARG 15 ENGINEERED MUTATION SEQRES 1 A 135 SER ASN VAL PRO HIS LYS SER SER LEU PRO GLU GLY ILE SEQRES 2 A 135 ALA PRO GLY THR VAL LEU ARG ILE ARG GLY LEU VAL PRO SEQRES 3 A 135 PRO ASN ALA SER ARG PHE HIS VAL ASN LEU LEU CYS GLY SEQRES 4 A 135 GLU GLU GLN GLY SER ASP ALA ALA LEU HIS PHE ASN PRO SEQRES 5 A 135 ARG LEU ASP THR SER GLU VAL VAL PHE ASN SER LYS GLU SEQRES 6 A 135 GLN GLY SER TRP GLY ARG GLU GLU ARG GLY PRO GLY VAL SEQRES 7 A 135 PRO PHE GLN ARG GLY GLN PRO PHE GLU VAL LEU ILE ILE SEQRES 8 A 135 ALA SER ASP ASP GLY PHE LYS ALA VAL VAL GLY ASP ALA SEQRES 9 A 135 GLN TYR HIS HIS PHE ARG HIS ARG LEU PRO LEU ALA ARG SEQRES 10 A 135 VAL ARG LEU VAL GLU VAL GLY GLY ASP VAL GLN LEU ASP SEQRES 11 A 135 SER VAL ARG ILE PHE SEQRES 1 B 135 SER ASN VAL PRO HIS LYS SER SER LEU PRO GLU GLY ILE SEQRES 2 B 135 ALA PRO GLY THR VAL LEU ARG ILE ARG GLY LEU VAL PRO SEQRES 3 B 135 PRO ASN ALA SER ARG PHE HIS VAL ASN LEU LEU CYS GLY SEQRES 4 B 135 GLU GLU GLN GLY SER ASP ALA ALA LEU HIS PHE ASN PRO SEQRES 5 B 135 ARG LEU ASP THR SER GLU VAL VAL PHE ASN SER LYS GLU SEQRES 6 B 135 GLN GLY SER TRP GLY ARG GLU GLU ARG GLY PRO GLY VAL SEQRES 7 B 135 PRO PHE GLN ARG GLY GLN PRO PHE GLU VAL LEU ILE ILE SEQRES 8 B 135 ALA SER ASP ASP GLY PHE LYS ALA VAL VAL GLY ASP ALA SEQRES 9 B 135 GLN TYR HIS HIS PHE ARG HIS ARG LEU PRO LEU ALA ARG SEQRES 10 B 135 VAL ARG LEU VAL GLU VAL GLY GLY ASP VAL GLN LEU ASP SEQRES 11 B 135 SER VAL ARG ILE PHE HET GOL A 201 14 HET PEG A 202 17 HET PEG A 203 17 HET GOL A 204 14 HET GOL A 205 14 HET GOL B 201 14 HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 4(C3 H8 O3) FORMUL 4 PEG 2(C4 H10 O3) FORMUL 9 HOH *216(H2 O) HELIX 1 AA1 PRO A 114 VAL A 118 5 5 HELIX 2 AA2 PRO B 114 VAL B 118 5 5 SHEET 1 AA1 6 HIS A 5 SER A 8 0 SHEET 2 AA1 6 LEU A 120 GLY A 125 -1 O VAL A 123 N HIS A 5 SHEET 3 AA1 6 PHE A 32 LEU A 37 -1 N ASN A 35 O GLU A 122 SHEET 4 AA1 6 ALA A 46 ARG A 53 -1 O PHE A 50 N VAL A 34 SHEET 5 AA1 6 GLU A 58 GLU A 65 -1 O GLU A 58 N ARG A 53 SHEET 6 AA1 6 SER A 68 TRP A 69 -1 O SER A 68 N GLU A 65 SHEET 1 AA2 6 HIS A 5 SER A 8 0 SHEET 2 AA2 6 LEU A 120 GLY A 125 -1 O VAL A 123 N HIS A 5 SHEET 3 AA2 6 PHE A 32 LEU A 37 -1 N ASN A 35 O GLU A 122 SHEET 4 AA2 6 ALA A 46 ARG A 53 -1 O PHE A 50 N VAL A 34 SHEET 5 AA2 6 GLU A 58 GLU A 65 -1 O GLU A 58 N ARG A 53 SHEET 6 AA2 6 GLU A 73 ARG A 74 -1 O GLU A 73 N PHE A 61 SHEET 1 AA3 5 ALA A 104 ARG A 110 0 SHEET 2 AA3 5 GLY A 96 VAL A 101 -1 N ALA A 99 O HIS A 107 SHEET 3 AA3 5 PRO A 85 ALA A 92 -1 N ILE A 91 O LYS A 98 SHEET 4 AA3 5 THR A 17 LEU A 24 -1 N ILE A 21 O VAL A 88 SHEET 5 AA3 5 GLN A 128 PHE A 135 -1 O ARG A 133 N ARG A 20 SHEET 1 AA4 6 HIS B 5 SER B 8 0 SHEET 2 AA4 6 LEU B 120 GLY B 125 -1 O VAL B 123 N HIS B 5 SHEET 3 AA4 6 PHE B 32 LEU B 37 -1 N LEU B 37 O LEU B 120 SHEET 4 AA4 6 ALA B 46 ARG B 53 -1 O LEU B 48 N LEU B 36 SHEET 5 AA4 6 GLU B 58 GLU B 65 -1 O GLU B 58 N ARG B 53 SHEET 6 AA4 6 SER B 68 TRP B 69 -1 O SER B 68 N GLU B 65 SHEET 1 AA5 6 HIS B 5 SER B 8 0 SHEET 2 AA5 6 LEU B 120 GLY B 125 -1 O VAL B 123 N HIS B 5 SHEET 3 AA5 6 PHE B 32 LEU B 37 -1 N LEU B 37 O LEU B 120 SHEET 4 AA5 6 ALA B 46 ARG B 53 -1 O LEU B 48 N LEU B 36 SHEET 5 AA5 6 GLU B 58 GLU B 65 -1 O GLU B 58 N ARG B 53 SHEET 6 AA5 6 GLU B 73 GLY B 75 -1 O GLY B 75 N VAL B 59 SHEET 1 AA6 5 ALA B 104 ARG B 110 0 SHEET 2 AA6 5 GLY B 96 VAL B 101 -1 N ALA B 99 O TYR B 106 SHEET 3 AA6 5 PRO B 85 ALA B 92 -1 N LEU B 89 O VAL B 100 SHEET 4 AA6 5 VAL B 18 LEU B 24 -1 N ILE B 21 O VAL B 88 SHEET 5 AA6 5 GLN B 128 PHE B 135 -1 O PHE B 135 N VAL B 18 CISPEP 1 VAL A 3 PRO A 4 0 6.68 CRYST1 53.750 64.950 70.410 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 0.018605 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015396 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014203 0.00000