HEADER ISOMERASE 27-APR-21 7EPO TITLE KETOSTEROID ISOMERASE KSI WITH 5-NITROBENZOXAZOLE (5NBI) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SNOAL-LIKE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: KETOSTEROID ISOMERASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS (STRAIN ATCC 700084 SOURCE 3 / MC(2)155); SOURCE 4 ORGANISM_COMMON: MYCOBACTERIUM SMEGMATIS; SOURCE 5 ORGANISM_TAXID: 246196; SOURCE 6 STRAIN: ATCC 700084 / MC(2)155; SOURCE 7 GENE: MSMEI_6677; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS KEMP ELIMINATION, MSKSI, MYCOBACTERIUM SMEGMATIS, CRYSTAL STRUCTURE., KEYWDS 2 ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIANG,Q.ZHANG,M.BARTLAM REVDAT 2 29-NOV-23 7EPO 1 REMARK REVDAT 1 22-DEC-21 7EPO 0 JRNL AUTH Y.LIANG,W.LI,H.LIANG,X.LOU,R.LIU,Q.ZHANG,M.BARTLAM JRNL TITL STRUCTURAL CHARACTERIZATION AND KEMP ELIMINASE ACTIVITY OF JRNL TITL 2 THE MYCOBACTERIUM SMEGMATIS KETOSTEROID ISOMERASE. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 560 159 2021 JRNL REFN ESSN 1090-2104 JRNL PMID 33992958 JRNL DOI 10.1016/J.BBRC.2021.05.007 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 6228 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 619 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 24.2100 - 3.7300 1.00 1468 163 0.1707 0.2107 REMARK 3 2 3.7300 - 2.9600 1.00 1391 154 0.2118 0.3071 REMARK 3 3 2.9600 - 2.5900 1.00 1383 151 0.2425 0.3783 REMARK 3 4 2.5900 - 2.3500 0.99 1367 151 0.2792 0.3916 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) : 0.425 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.749 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 70.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 82.95 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 1051 REMARK 3 ANGLE : 0.829 1430 REMARK 3 CHIRALITY : 0.055 158 REMARK 3 PLANARITY : 0.007 186 REMARK 3 DIHEDRAL : 5.997 142 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): -27.6370 4.5945 0.8536 REMARK 3 T TENSOR REMARK 3 T11: 0.5618 T22: 0.5273 REMARK 3 T33: 0.5021 T12: -0.0803 REMARK 3 T13: -0.0202 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 4.7340 L22: 6.6477 REMARK 3 L33: 4.5816 L12: 0.1602 REMARK 3 L13: 0.3366 L23: -2.0082 REMARK 3 S TENSOR REMARK 3 S11: -0.1853 S12: 0.5300 S13: -0.0181 REMARK 3 S21: -0.6930 S22: 0.1394 S23: -0.0952 REMARK 3 S31: 0.0657 S32: -0.0717 S33: 0.0741 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 7EPO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1300021977. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 0.9793 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-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6258 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 18.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.290 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 7EPN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M REMARK 280 TRIS, PH 8.5, 30% (W/V) PEG 3000, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.33267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.16633 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.16633 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.33267 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 23.16633 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 HIS A 69 REMARK 465 VAL A 70 REMARK 465 ALA A 71 REMARK 465 LYS A 72 REMARK 465 GLN A 73 REMARK 465 ALA A 137 REMARK 465 GLU A 138 REMARK 465 ASN A 139 REMARK 465 ALA A 140 REMARK 465 GLY A 141 REMARK 465 GLU A 142 REMARK 465 PRO A 143 REMARK 465 VAL A 144 REMARK 465 ARG A 145 REMARK 465 SER A 146 REMARK 465 ARG A 147 REMARK 465 ALA A 148 REMARK 465 SER A 149 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 ILE A 49 94.68 -65.33 REMARK 500 ASP A 128 83.32 -66.43 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 H5J A 201 DBREF 7EPO A 1 149 UNP I7FVV8 I7FVV8_MYCS2 1 149 SEQRES 1 A 149 MET VAL SER THR ARG GLU THR VAL ASN GLU LEU LEU ARG SEQRES 2 A 149 ARG ILE ALA ALA GLY ASP PRO GLY ARG ILE ALA GLU LEU SEQRES 3 A 149 TYR ALA GLU GLU VAL SER TRP LYS LEU SER TRP PRO ALA SEQRES 4 A 149 GLY ASP HIS MET GLY VAL VAL PRO TRP ILE GLN GLN ARG SEQRES 5 A 149 SER THR ARG ALA GLY VAL GLU GLU HIS PHE ARG LEU ILE SEQRES 6 A 149 ALA ASP HIS HIS VAL ALA LYS GLN SER SER ALA GLU VAL SEQRES 7 A 149 PHE SER VAL LEU VAL ASP GLY ALA ASP ALA VAL VAL LEU SEQRES 8 A 149 GLY GLU LEU ARG ASN THR ALA GLY PRO THR GLY ARG SER SEQRES 9 A 149 TYR GLU ALA PRO PHE ALA LEU HIS LEU THR VAL GLU ASN SEQRES 10 A 149 GLY LEU VAL THR ARG HIS HIS VAL TYR GLU ASP SER LEU SEQRES 11 A 149 ALA VAL PHE ARG ALA PHE ALA GLU ASN ALA GLY GLU PRO SEQRES 12 A 149 VAL ARG SER ARG ALA SER HET H5J A 201 12 HETNAM H5J 5-NITRO-1,2-BENZOXAZOLE FORMUL 2 H5J C7 H4 N2 O3 FORMUL 3 HOH *30(H2 O) HELIX 1 AA1 SER A 3 GLY A 18 1 16 HELIX 2 AA2 ASP A 19 LEU A 26 1 8 HELIX 3 AA3 PRO A 38 HIS A 42 5 5 HELIX 4 AA4 THR A 54 HIS A 68 1 15 HELIX 5 AA5 ASP A 128 ALA A 135 1 8 SHEET 1 AA1 5 TYR A 27 LEU A 35 0 SHEET 2 AA1 5 LEU A 119 GLU A 127 1 O VAL A 120 N ALA A 28 SHEET 3 AA1 5 SER A 104 GLU A 116 -1 N ALA A 110 O TYR A 126 SHEET 4 AA1 5 ASP A 87 THR A 97 -1 N ALA A 88 O LEU A 113 SHEET 5 AA1 5 SER A 75 ASP A 84 -1 N ASP A 84 O ASP A 87 SITE 1 AC1 6 TRP A 48 HIS A 61 LEU A 94 HIS A 123 SITE 2 AC1 6 VAL A 125 GLU A 127 CRYST1 59.636 59.636 69.499 90.00 90.00 120.00 P 32 2 1 6 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 0.016768 0.009681 0.000000 0.00000 SCALE2 0.000000 0.019362 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014389 0.00000