HEADER LIPID BINDING PROTEIN 12-DEC-21 7WA9 TITLE CRYSTAL STRUCTURE OF MSMEG_5634 FROM MYCOBACTERIUM SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MSMEG_5634; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: ATCC 700084 / MC(2)155; SOURCE 5 GENE: MSMEG_5634; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MSMEG_5634, ACYL-ACPM, FAS-II INHIBITOR, MYCOBACTERIUM SMEGMATIS, KEYWDS 2 LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.WANG,W.ZHANG REVDAT 1 19-OCT-22 7WA9 0 JRNL AUTH M.LI,Q.HUANG,W.ZHANG,Y.CAO,Z.WANG,Z.ZHAO,X.ZHANG,J.ZHANG JRNL TITL A NOVEL ACYL-ACPM-BINDING PROTEIN CONFERS INTRINSIC JRNL TITL 2 SENSITIVITY TO FATTY ACID SYNTHASE TYPE II INHIBITORS IN JRNL TITL 3 MYCOBACTERIUM SMEGMATIS JRNL REF FRONT MICROBIOL V. 13 46722 2022 JRNL REFN ESSN 1664-302X JRNL PMID 35444621 JRNL DOI 10.3389/FMICB.2022.846722 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 11339 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 542 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 22.1900 - 3.0200 0.98 2717 145 0.2221 0.2574 REMARK 3 2 3.0200 - 2.4000 1.00 2723 126 0.2611 0.3076 REMARK 3 3 2.4000 - 2.0900 0.99 2695 131 0.2317 0.2902 REMARK 3 4 2.0900 - 1.9000 0.98 2662 140 0.2289 0.3222 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) : 0.279 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.841 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.19 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 1148 REMARK 3 ANGLE : 1.095 1557 REMARK 3 CHIRALITY : 0.063 174 REMARK 3 PLANARITY : 0.006 196 REMARK 3 DIHEDRAL : 15.266 426 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 7WA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1300026286. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21971 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.59600 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM ACETATE HYDRATE, 20% W/V REMARK 280 POLYETHYLENE GLYCOL 3350, PH 7.5, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.53600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.50550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.53600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.50550 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 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 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 PRO A 144 REMARK 465 SER A 145 REMARK 465 ALA A 146 REMARK 465 THR A 147 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 79 CA - CB - CG ANGL. DEV. = 17.9 DEGREES 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 PRO A 74 40.49 -98.74 REMARK 500 REMARK 500 REMARK: NULL DBREF 7WA9 A 1 147 UNP A0R3Y0 A0R3Y0_MYCS2 1 147 SEQADV 7WA9 SER A 0 UNP A0R3Y0 EXPRESSION TAG SEQRES 1 A 148 SER MSE ALA LYS LEU SER VAL SER VAL GLU VAL PRO LEU SEQRES 2 A 148 PRO PRO GLU GLN ALA TRP GLU TYR ALA SER ASP LEU SER SEQRES 3 A 148 ARG TYR HIS GLU TRP LEU SER ILE HIS ARG ALA TRP ARG SEQRES 4 A 148 SER LYS LEU PRO GLU THR LEU GLU LYS GLY THR VAL ILE SEQRES 5 A 148 GLU SER ILE VAL GLU VAL LYS GLY MSE LEU ASN ARG VAL SEQRES 6 A 148 ARG TRP THR LEU VAL HIS TYR LYS PRO PRO GLN ALA LEU SEQRES 7 A 148 THR LEU ASN GLY ASP GLY ARG GLY GLY VAL LYS VAL LYS SEQRES 8 A 148 LEU ILE GLY LYS ILE LYS PRO THR ASP ASN GLY ALA THR SEQRES 9 A 148 VAL GLY PHE ASP LEU HIS LEU GLY GLY PRO ALA LEU PHE SEQRES 10 A 148 GLY PRO ILE GLY MSE VAL VAL ALA ALA ALA LEU LYS SER SEQRES 11 A 148 ASP ILE GLN GLU SER LEU ASN ARG PHE LYS GLN LEU TYR SEQRES 12 A 148 ALA PRO SER ALA THR MODRES 7WA9 MSE A 1 MET MODIFIED RESIDUE MODRES 7WA9 MSE A 60 MET MODIFIED RESIDUE MODRES 7WA9 MSE A 121 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 60 8 HET MSE A 121 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *52(H2 O) HELIX 1 AA1 PRO A 13 SER A 22 1 10 HELIX 2 AA2 ASP A 23 TRP A 30 5 8 HELIX 3 AA3 GLY A 112 GLY A 117 1 6 HELIX 4 AA4 ILE A 119 ALA A 143 1 25 SHEET 1 AA1 7 LYS A 3 VAL A 10 0 SHEET 2 AA1 7 GLY A 101 GLY A 111 -1 O PHE A 106 N VAL A 6 SHEET 3 AA1 7 VAL A 87 THR A 98 -1 N ILE A 92 O ASP A 107 SHEET 4 AA1 7 ALA A 76 GLY A 83 -1 N LEU A 77 O GLY A 93 SHEET 5 AA1 7 MSE A 60 LYS A 72 -1 N LYS A 72 O ALA A 76 SHEET 6 AA1 7 VAL A 50 VAL A 57 -1 N ILE A 51 O TRP A 66 SHEET 7 AA1 7 HIS A 34 TRP A 37 -1 N ALA A 36 O ILE A 54 LINK C SER A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N ALA A 2 1555 1555 1.33 LINK C GLY A 59 N MSE A 60 1555 1555 1.33 LINK C MSE A 60 N LEU A 61 1555 1555 1.33 LINK C GLY A 120 N MSE A 121 1555 1555 1.33 LINK C MSE A 121 N VAL A 122 1555 1555 1.34 CISPEP 1 PRO A 73 PRO A 74 0 -4.23 CRYST1 71.072 55.011 40.733 90.00 112.75 90.00 C 1 2 1 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 0.014070 0.000000 0.005901 0.00000 SCALE2 0.000000 0.018178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026622 0.00000