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 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. 2024
JRNL REFN ESSN 1083-351X
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