HEADER LIGASE 05-JAN-24 8VIR TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF FATTY ACID KINASE A TITLE 2 (FAKA) FROM STAPHYLOCOCCUS AUREUS (APO) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID KINASE A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (M1-A212); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325; SOURCE 3 ORGANISM_TAXID: 93061; SOURCE 4 GENE: SAOUHSC_01193; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS FATTY ACID KINASE A, STAPHYLOCOCCUS AUREUS, MRSA, PROLINE KEYWDS 2 ISOMERIZATION, FATTY ACID METABOLISM, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LOVELL,M.M.KASHIPATHY,K.P.BATTAILE,J.L.BOSE REVDAT 2 13-NOV-24 8VIR 1 JRNL REVDAT 1 06-NOV-24 8VIR 0 JRNL AUTH M.J.MYERS,Z.XU,B.J.RYAN,Z.R.DEMARS,M.J.RIDDER,D.K.JOHNSON, JRNL AUTH 2 C.N.KRUTE,T.S.FLYNN,M.M.KASHIPATHY,K.P.BATTAILE,N.SCHNICKER, JRNL AUTH 3 S.LOVELL,B.D.FREUDENTHAL,J.L.BOSE JRNL TITL MOLECULAR INSIGHTS INTO THE STRUCTURE AND FUNCTION OF THE JRNL TITL 2 STAPHYLOCOCCUS AUREUS FATTY ACID KINASE. JRNL REF J.BIOL.CHEM. 07920 2024 JRNL REFN ESSN 1083-351X JRNL PMID 39454961 JRNL DOI 10.1016/J.JBC.2024.107920 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_3479: ???) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.160 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15310 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 726 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 42.3500 - 3.2486 1.00 3048 167 0.1523 0.1822 REMARK 3 2 3.2486 - 2.5786 1.00 2921 150 0.1737 0.2444 REMARK 3 3 2.5786 - 2.2527 1.00 2877 137 0.1847 0.2335 REMARK 3 4 2.2527 - 2.0467 1.00 2883 129 0.2053 0.2527 REMARK 3 5 2.0467 - 1.9000 1.00 2855 143 0.2403 0.3289 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 1540 REMARK 3 ANGLE : 0.921 2088 REMARK 3 CHIRALITY : 0.052 254 REMARK 3 PLANARITY : 0.006 276 REMARK 3 DIHEDRAL : 11.399 936 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 8VIR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000280330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI 111 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15360 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 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) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 1.12900 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROPLEX D1: 25% (W/V) PEG 4000, 100 MM REMARK 280 HEPES PH 7.5, 200 MM NACL, CRYO: 80% WELL SOLUTION AND 20% (V/V) REMARK 280 PEG 200., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 21.02400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.61600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.76900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.61600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.02400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.76900 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 VAL A 211 REMARK 465 ALA A 212 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 0 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 4 CG CD CE NZ REMARK 470 LYS A 8 CD CE NZ REMARK 470 LYS A 62 CE NZ REMARK 470 LYS A 73 CD CE NZ REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 LYS A 122 CE NZ REMARK 470 MET A 125 CG SD CE REMARK 470 LYS A 126 CG CD CE NZ REMARK 470 GLU A 151 CG CD OE1 OE2 REMARK 470 LYS A 179 CD CE NZ REMARK 470 LYS A 203 CE NZ REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 GLU A 208 CG CD OE1 OE2 REMARK 470 LYS A 210 CG CD CE NZ 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 LYS A 126 81.77 64.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 8VIR A 1 212 UNP Q2FZ58 Y1193_STAA8 1 212 SEQADV 8VIR MET A -19 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR GLY A -18 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR SER A -17 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR SER A -16 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR HIS A -15 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR HIS A -14 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR HIS A -13 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR HIS A -12 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR HIS A -11 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR HIS A -10 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR SER A -9 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR SER A -8 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR GLY A -7 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR LEU A -6 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR VAL A -5 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR PRO A -4 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR ARG A -3 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR GLY A -2 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR SER A -1 UNP Q2FZ58 EXPRESSION TAG SEQADV 8VIR HIS A 0 UNP Q2FZ58 EXPRESSION TAG SEQRES 1 A 232 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 232 LEU VAL PRO ARG GLY SER HIS MET ILE SER LYS ILE ASN SEQRES 3 A 232 GLY LYS LEU PHE ALA ASP MET ILE ILE GLN GLY ALA GLN SEQRES 4 A 232 ASN LEU SER ASN ASN ALA ASP LEU VAL ASP SER LEU ASN SEQRES 5 A 232 VAL TYR PRO VAL PRO ASP GLY ASP THR GLY THR ASN MET SEQRES 6 A 232 ASN LEU THR MET THR SER GLY ARG GLU GLU VAL GLU ASN SEQRES 7 A 232 ASN LEU SER LYS ASN ILE GLY GLU LEU GLY LYS THR PHE SEQRES 8 A 232 SER LYS GLY LEU LEU MET GLY ALA ARG GLY ASN SER GLY SEQRES 9 A 232 VAL ILE LEU SER GLN LEU PHE ARG GLY PHE CYS LYS ASN SEQRES 10 A 232 ILE GLU SER GLU SER GLU ILE ASN SER LYS LEU LEU ALA SEQRES 11 A 232 GLU SER PHE GLN ALA GLY VAL GLU THR ALA TYR LYS ALA SEQRES 12 A 232 VAL MET LYS PRO VAL GLU GLY THR ILE LEU THR VAL ALA SEQRES 13 A 232 LYS ASP ALA ALA GLN ALA ALA ILE GLU LYS ALA ASN ASN SEQRES 14 A 232 THR GLU ASP CYS ILE GLU LEU MET GLU TYR ILE ILE VAL SEQRES 15 A 232 LYS ALA ASN GLU SER LEU GLU ASN THR PRO ASN LEU LEU SEQRES 16 A 232 ALA VAL LEU LYS GLU VAL GLY VAL VAL ASP SER GLY GLY SEQRES 17 A 232 LYS GLY LEU LEU CYS VAL TYR GLU GLY PHE LEU LYS ALA SEQRES 18 A 232 LEU LYS GLY GLU LYS VAL GLU ALA LYS VAL ALA FORMUL 2 HOH *85(H2 O) HELIX 1 AA1 GLY A 7 ASN A 24 1 18 HELIX 2 AA2 ASN A 24 ASN A 32 1 9 HELIX 3 AA3 ASP A 40 ASN A 59 1 20 HELIX 4 AA4 ASN A 63 ALA A 79 1 17 HELIX 5 AA5 ARG A 80 GLU A 99 1 20 HELIX 6 AA6 ASN A 105 ALA A 123 1 19 HELIX 7 AA7 THR A 131 ASN A 148 1 18 HELIX 8 AA8 ASP A 152 THR A 171 1 20 HELIX 9 AA9 PRO A 172 LEU A 174 5 3 HELIX 10 AB1 LEU A 175 GLY A 182 1 8 HELIX 11 AB2 ASP A 185 GLY A 204 1 20 SHEET 1 AA1 2 ILE A 5 ASN A 6 0 SHEET 2 AA1 2 GLU A 103 ILE A 104 -1 O ILE A 104 N ILE A 5 CRYST1 42.048 47.538 93.232 90.00 90.00 90.00 P 21 21 21 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 0.023782 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021036 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010726 0.00000