HEADER SUGAR BINDING PROTEIN 04-JUN-21 7N57 TITLE CRYSTAL STRUCTURE OF R20A HUMAN GALECTIN-7 MUTANT IN PRESENCE OF TITLE 2 LACTOSE 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 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 7N57 1 REMARK REVDAT 1 25-JAN-23 7N57 0 JRNL AUTH N.T.H.PHAM,C.CALMETTES,N.DOUCET JRNL TITL CRYSTAL STRUCTURE OF R20A HUMAN GALECTIN-7 MUTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.83 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) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23493 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1175 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 44.9100 - 3.6600 1.00 2986 158 0.1657 0.1964 REMARK 3 2 3.6600 - 2.9100 1.00 2815 148 0.1627 0.2094 REMARK 3 3 2.9000 - 2.5400 1.00 2767 145 0.1830 0.2005 REMARK 3 4 2.5400 - 2.3100 1.00 2759 146 0.1721 0.1940 REMARK 3 5 2.3100 - 2.1400 1.00 2769 145 0.1650 0.2204 REMARK 3 6 2.1400 - 2.0100 1.00 2723 144 0.1791 0.2131 REMARK 3 7 2.0100 - 1.9100 1.00 2747 144 0.1801 0.2407 REMARK 3 8 1.9100 - 1.8300 1.00 2752 145 0.1904 0.2487 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.53 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 : 0.011 2255 REMARK 3 ANGLE : 1.206 3071 REMARK 3 CHIRALITY : 0.068 339 REMARK 3 PLANARITY : 0.008 410 REMARK 3 DIHEDRAL : 14.067 832 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 7N57 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000256807. 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45632 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 44.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.064 REMARK 200 R MERGE (I) : 0.18600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 1.75500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.010 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: 4GAL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM CHLORIDE, 0.1M TRIS PH REMARK 280 8.0, 20% W/V PEG 6000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K 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 15.11000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.59500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.09500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.59500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.11000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.09500 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, D, E 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 SER B 1 REMARK 465 ASN B 2 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 PRO A 79 34.58 -90.37 REMARK 500 SER B 30 -62.43 -98.86 REMARK 500 SER B 30 -62.70 -98.67 REMARK 500 PRO B 79 43.61 -85.78 REMARK 500 REMARK 500 REMARK: NULL DBREF 7N57 A 1 135 UNP P47929 LEG7_HUMAN 2 136 DBREF 7N57 B 1 135 UNP P47929 LEG7_HUMAN 2 136 SEQADV 7N57 ALA A 20 UNP P47929 ARG 21 ENGINEERED MUTATION SEQADV 7N57 ALA B 20 UNP P47929 ARG 21 ENGINEERED MUTATION SEQRES 1 A 135 SER ASN VAL PRO HIS LYS SER SER LEU PRO GLU GLY ILE SEQRES 2 A 135 ARG PRO GLY THR VAL LEU ALA 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 ARG PRO GLY THR VAL LEU ALA 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 GLC D 1 22 HET GAL D 2 22 HET GLC E 1 23 HET GAL E 2 22 HET GOL A 201 14 HET EDO A 202 10 HET EDO B 301 10 HET EDO B 302 10 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 GLC 2(C6 H12 O6) FORMUL 3 GAL 2(C6 H12 O6) FORMUL 5 GOL C3 H8 O3 FORMUL 6 EDO 3(C2 H6 O2) FORMUL 9 HOH *187(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 LEU A 48 N LEU A 36 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 LEU A 48 N LEU A 36 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 LEU A 89 O VAL A 100 SHEET 4 AA3 5 VAL A 18 LEU A 24 -1 N ILE A 21 O VAL A 88 SHEET 5 AA3 5 GLN A 128 PHE A 135 -1 O PHE A 135 N VAL A 18 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 ASN B 35 O GLU B 122 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 ASN B 35 O GLU B 122 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 ARG B 74 -1 O GLU B 73 N PHE B 61 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 HIS B 107 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 LEU B 19 O ILE B 90 SHEET 5 AA6 5 GLN B 128 PHE B 135 -1 O PHE B 135 N VAL B 18 LINK O4 GLC D 1 C1 GAL D 2 1555 1555 1.38 LINK O4 GLC E 1 C1 GAL E 2 1555 1555 1.37 CRYST1 30.220 76.190 111.190 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 0.033091 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013125 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008994 0.00000