HEADER LIGASE 26-OCT-15 5FLG TITLE CRYSTAL STRUCTURE OF THE 6-CARBOXYHEXANOATE-COA LIGASE (BIOW)FROM TITLE 2 BACILLUS SUBTILIS IN COMPLEX WITH AMPPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6-CARBOXYHEXANOATE--COA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PIMELOYL-COA SYNTHASE; COMPND 5 EC: 6.2.1.14; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR L.MOYNIE,M.WANG,D.J.CAMPOPIANO,J.H.NAISMITH REVDAT 5 08-MAY-24 5FLG 1 REMARK LINK REVDAT 4 24-MAY-17 5FLG 1 JRNL REVDAT 3 26-APR-17 5FLG 1 JRNL REVDAT 2 12-APR-17 5FLG 1 JRNL REVDAT 1 16-NOV-16 5FLG 0 JRNL AUTH M.WANG,L.MOYNIE,P.J.HARRISON,V.KELLY,A.PIPER,J.H.NAISMITH, JRNL AUTH 2 D.J.CAMPOPIANO JRNL TITL USING THE PIMELOYL-COA SYNTHETASE ADENYLATION FOLD TO JRNL TITL 2 SYNTHESIZE FATTY ACID THIOESTERS. JRNL REF NAT. CHEM. BIOL. V. 13 660 2017 JRNL REFN ESSN 1552-4469 JRNL PMID 28414710 JRNL DOI 10.1038/NCHEMBIO.2361 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 39459 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2017 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2655 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.3510 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4054 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 72 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.44000 REMARK 3 B22 (A**2) : -2.46000 REMARK 3 B33 (A**2) : -0.97000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.182 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.158 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.667 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4250 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3947 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5745 ; 1.309 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9134 ; 0.722 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 506 ; 7.455 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 208 ;38.143 ;24.087 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 749 ;14.572 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;20.799 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 597 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4732 ; 0.017 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 968 ; 0.007 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 5 255 B 5 255 14898 0.12 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 5FLG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1290065371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-14 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 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 : 41543 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 55.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 MM HEPES PH 7.5 19 % PEG 400 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 24.79500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 83.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.79500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.95000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 0 REMARK 465 ALA A 1 REMARK 465 MET A 2 REMARK 465 GLU A 3 REMARK 465 HIS A 20 REMARK 465 GLU A 21 REMARK 465 SER A 259 REMARK 465 GLY B 0 REMARK 465 ALA B 1 REMARK 465 MET B 2 REMARK 465 GLU B 3 REMARK 465 GLU B 4 REMARK 465 HIS B 257 REMARK 465 ASP B 258 REMARK 465 SER B 259 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2039 O HOH A 2042 2.02 REMARK 500 O71 PML A 701 O HOH A 2032 2.07 REMARK 500 O THR B 6 O HOH B 2001 2.19 REMARK 500 O VAL A 122 O HOH A 2025 2.19 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 LYS A 140 -128.30 54.26 REMARK 500 HIS A 257 45.49 -76.54 REMARK 500 LYS B 140 -126.51 52.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 227 0.10 SIDE CHAIN REMARK 500 ARG B 227 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 704 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 195 OD1 REMARK 620 2 ASP A 196 OD1 102.1 REMARK 620 3 ANP A 702 O1A 80.9 108.8 REMARK 620 4 ANP A 702 O3A 85.4 163.0 56.9 REMARK 620 5 ANP A 702 O2G 167.9 89.9 94.0 82.7 REMARK 620 6 HOH A2006 O 88.0 115.1 136.1 80.0 88.1 REMARK 620 7 HOH A2039 O 127.4 74.8 53.1 88.5 54.3 141.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ANP A 702 O2A REMARK 620 2 ANP A 702 O1B 80.6 REMARK 620 3 ANP A 702 O3G 87.7 83.9 REMARK 620 4 HOH A2007 O 170.8 91.9 86.1 REMARK 620 5 HOH A2033 O 91.8 172.4 95.8 95.7 REMARK 620 6 HOH A2043 O 92.6 88.3 172.1 92.5 92.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 704 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 195 OD1 REMARK 620 2 ASP B 196 OD1 98.4 REMARK 620 3 ANP B 702 O1A 84.9 107.4 REMARK 620 4 ANP B 702 O1G 171.3 90.2 91.2 REMARK 620 5 ANP B 702 O3A 86.0 161.4 54.7 85.4 REMARK 620 6 HOH B2005 O 88.8 111.6 141.0 89.4 86.4 REMARK 620 7 HOH B2025 O 129.4 73.5 53.1 51.9 89.7 141.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ANP B 702 O2G REMARK 620 2 ANP B 702 O1B 87.4 REMARK 620 3 ANP B 702 O2A 86.1 89.0 REMARK 620 4 HOH B2006 O 91.6 92.2 177.4 REMARK 620 5 HOH B2019 O 97.3 175.1 89.8 89.2 REMARK 620 6 HOH B2029 O 172.6 85.8 90.8 91.6 89.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PML A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PML B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 704 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FLL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 6-CARBOXYHEXANOATE-COA LIGASE (BIOW)FROM REMARK 900 BACILLUS SUBTILIS IN COMPLEX WITH A PIMELOYL-ADENYLATE REMARK 900 RELATED ID: 5FM0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 6-CARBOXYHEXANOATE-COA LIGASE (BIOW)FROM REMARK 900 BACILLUS SUBTILIS (PTCL4 DERIVATIVE) DBREF 5FLG A 4 259 UNP P53559 BIOW_BACSU 4 259 DBREF 5FLG B 4 259 UNP P53559 BIOW_BACSU 4 259 SEQADV 5FLG GLY A 0 UNP P53559 EXPRESSION TAG SEQADV 5FLG ALA A 1 UNP P53559 EXPRESSION TAG SEQADV 5FLG MET A 2 UNP P53559 EXPRESSION TAG SEQADV 5FLG GLU A 3 UNP P53559 EXPRESSION TAG SEQADV 5FLG GLY B 0 UNP P53559 EXPRESSION TAG SEQADV 5FLG ALA B 1 UNP P53559 EXPRESSION TAG SEQADV 5FLG MET B 2 UNP P53559 EXPRESSION TAG SEQADV 5FLG GLU B 3 UNP P53559 EXPRESSION TAG SEQRES 1 A 260 GLY ALA MET GLU GLU GLU THR PHE TYR SER VAL ARG MET SEQRES 2 A 260 ARG ALA SER MET ASN GLY SER HIS GLU ASP GLY GLY LYS SEQRES 3 A 260 HIS ILE SER GLY GLY GLU ARG LEU ILE PRO PHE HIS GLU SEQRES 4 A 260 MET LYS HIS THR VAL ASN ALA LEU LEU GLU LYS GLY LEU SEQRES 5 A 260 SER HIS SER ARG GLY LYS PRO ASP PHE MET GLN ILE GLN SEQRES 6 A 260 PHE GLU GLU VAL HIS GLU SER ILE LYS THR ILE GLN PRO SEQRES 7 A 260 LEU PRO VAL HIS THR ASN GLU VAL SER CYS PRO GLU GLU SEQRES 8 A 260 GLY GLN LYS LEU ALA ARG LEU LEU LEU GLU LYS GLU GLY SEQRES 9 A 260 VAL SER ARG ASP VAL ILE GLU LYS ALA TYR GLU GLN ILE SEQRES 10 A 260 PRO GLU TRP SER ASP VAL ARG GLY ALA VAL LEU PHE ASP SEQRES 11 A 260 ILE HIS THR GLY LYS ARG MET ASP GLN THR LYS GLU LYS SEQRES 12 A 260 GLY VAL ARG VAL SER ARG MET ASP TRP PRO ASP ALA ASN SEQRES 13 A 260 PHE GLU LYS TRP ALA LEU HIS SER HIS VAL PRO ALA HIS SEQRES 14 A 260 SER ARG ILE LYS GLU ALA LEU ALA LEU ALA SER LYS VAL SEQRES 15 A 260 SER ARG HIS PRO ALA VAL VAL ALA GLU LEU CYS TRP SER SEQRES 16 A 260 ASP ASP PRO ASP TYR ILE THR GLY TYR VAL ALA GLY LYS SEQRES 17 A 260 LYS MET GLY TYR GLN ARG ILE THR ALA MET LYS GLU TYR SEQRES 18 A 260 GLY THR GLU GLU GLY CYS ARG VAL PHE PHE ILE ASP GLY SEQRES 19 A 260 SER ASN ASP VAL ASN THR TYR ILE HIS ASP LEU GLU LYS SEQRES 20 A 260 GLN PRO ILE LEU ILE GLU TRP GLU GLU ASP HIS ASP SER SEQRES 1 B 260 GLY ALA MET GLU GLU GLU THR PHE TYR SER VAL ARG MET SEQRES 2 B 260 ARG ALA SER MET ASN GLY SER HIS GLU ASP GLY GLY LYS SEQRES 3 B 260 HIS ILE SER GLY GLY GLU ARG LEU ILE PRO PHE HIS GLU SEQRES 4 B 260 MET LYS HIS THR VAL ASN ALA LEU LEU GLU LYS GLY LEU SEQRES 5 B 260 SER HIS SER ARG GLY LYS PRO ASP PHE MET GLN ILE GLN SEQRES 6 B 260 PHE GLU GLU VAL HIS GLU SER ILE LYS THR ILE GLN PRO SEQRES 7 B 260 LEU PRO VAL HIS THR ASN GLU VAL SER CYS PRO GLU GLU SEQRES 8 B 260 GLY GLN LYS LEU ALA ARG LEU LEU LEU GLU LYS GLU GLY SEQRES 9 B 260 VAL SER ARG ASP VAL ILE GLU LYS ALA TYR GLU GLN ILE SEQRES 10 B 260 PRO GLU TRP SER ASP VAL ARG GLY ALA VAL LEU PHE ASP SEQRES 11 B 260 ILE HIS THR GLY LYS ARG MET ASP GLN THR LYS GLU LYS SEQRES 12 B 260 GLY VAL ARG VAL SER ARG MET ASP TRP PRO ASP ALA ASN SEQRES 13 B 260 PHE GLU LYS TRP ALA LEU HIS SER HIS VAL PRO ALA HIS SEQRES 14 B 260 SER ARG ILE LYS GLU ALA LEU ALA LEU ALA SER LYS VAL SEQRES 15 B 260 SER ARG HIS PRO ALA VAL VAL ALA GLU LEU CYS TRP SER SEQRES 16 B 260 ASP ASP PRO ASP TYR ILE THR GLY TYR VAL ALA GLY LYS SEQRES 17 B 260 LYS MET GLY TYR GLN ARG ILE THR ALA MET LYS GLU TYR SEQRES 18 B 260 GLY THR GLU GLU GLY CYS ARG VAL PHE PHE ILE ASP GLY SEQRES 19 B 260 SER ASN ASP VAL ASN THR TYR ILE HIS ASP LEU GLU LYS SEQRES 20 B 260 GLN PRO ILE LEU ILE GLU TRP GLU GLU ASP HIS ASP SER HET PML A 701 11 HET ANP A 702 31 HET MG A 703 1 HET MG A 704 1 HET PML B 701 11 HET ANP B 702 31 HET MG B 703 1 HET MG B 704 1 HETNAM PML PIMELIC ACID HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 3 PML 2(C7 H12 O4) FORMUL 4 ANP 2(C10 H17 N6 O12 P3) FORMUL 5 MG 4(MG 2+) FORMUL 11 HOH *72(H2 O) HELIX 1 1 GLU A 38 SER A 52 1 15 HELIX 2 2 CYS A 87 GLU A 102 1 16 HELIX 3 3 SER A 105 ILE A 116 1 12 HELIX 4 4 PRO A 117 SER A 120 5 4 HELIX 5 5 PRO A 152 HIS A 164 1 13 HELIX 6 6 HIS A 168 HIS A 184 1 17 HELIX 7 7 ASP A 236 GLN A 247 1 12 HELIX 8 8 SER B 19 GLY B 23 5 5 HELIX 9 9 GLU B 38 SER B 52 1 15 HELIX 10 10 CYS B 87 GLU B 102 1 16 HELIX 11 11 SER B 105 ILE B 116 1 12 HELIX 12 12 PRO B 117 SER B 120 5 4 HELIX 13 13 PRO B 152 HIS B 164 1 13 HELIX 14 14 HIS B 168 HIS B 184 1 17 HELIX 15 15 ASP B 236 GLN B 247 1 12 SHEET 1 AA 6 LYS A 25 PRO A 35 0 SHEET 2 AA 6 PHE A 7 MET A 16 -1 O TYR A 8 N ILE A 34 SHEET 3 AA 6 PHE A 60 GLU A 67 -1 O PHE A 60 N SER A 15 SHEET 4 AA 6 PHE B 60 GLU B 67 -1 O MET B 61 N PHE A 65 SHEET 5 AA 6 PHE B 7 MET B 16 -1 O SER B 9 N GLU B 66 SHEET 6 AA 6 LYS B 25 PRO B 35 -1 O LYS B 25 N MET B 16 SHEET 1 AB 3 LYS A 73 ILE A 75 0 SHEET 2 AB 3 ILE A 249 ILE A 251 1 O LEU A 250 N ILE A 75 SHEET 3 AB 3 MET A 149 ASP A 150 1 O ASP A 150 N ILE A 251 SHEET 1 AC 7 VAL A 80 ASN A 83 0 SHEET 2 AC 7 GLY A 210 ILE A 214 1 O TYR A 211 N HIS A 81 SHEET 3 AC 7 GLY A 202 GLY A 206 -1 O GLY A 202 N ILE A 214 SHEET 4 AC 7 VAL A 187 TRP A 193 -1 O GLU A 190 N ALA A 205 SHEET 5 AC 7 CYS A 226 ILE A 231 -1 O CYS A 226 N TRP A 193 SHEET 6 AC 7 VAL A 126 ASP A 129 1 O VAL A 126 N PHE A 229 SHEET 7 AC 7 LYS A 134 ARG A 135 -1 O LYS A 134 N ASP A 129 SHEET 1 BA 3 LYS B 73 ILE B 75 0 SHEET 2 BA 3 ILE B 249 ILE B 251 1 O LEU B 250 N ILE B 75 SHEET 3 BA 3 MET B 149 ASP B 150 1 O ASP B 150 N ILE B 251 SHEET 1 BB 6 VAL B 80 ASN B 83 0 SHEET 2 BB 6 GLY B 210 ILE B 214 1 O TYR B 211 N HIS B 81 SHEET 3 BB 6 GLY B 202 GLY B 206 -1 O GLY B 202 N ILE B 214 SHEET 4 BB 6 VAL B 187 TRP B 193 -1 O GLU B 190 N ALA B 205 SHEET 5 BB 6 CYS B 226 ILE B 231 -1 O CYS B 226 N TRP B 193 SHEET 6 BB 6 VAL B 126 ASP B 129 1 O VAL B 126 N PHE B 229 LINK OD1 ASP A 195 MG MG A 704 1555 1555 2.24 LINK OD1 ASP A 196 MG MG A 704 1555 1555 2.24 LINK O2A ANP A 702 MG MG A 703 1555 1555 1.98 LINK O1B ANP A 702 MG MG A 703 1555 1555 1.98 LINK O3G ANP A 702 MG MG A 703 1555 1555 2.13 LINK O1A ANP A 702 MG MG A 704 1555 1555 2.57 LINK O3A ANP A 702 MG MG A 704 1555 1555 2.73 LINK O2G ANP A 702 MG MG A 704 1555 1555 2.31 LINK MG MG A 703 O HOH A2007 1555 1555 2.15 LINK MG MG A 703 O HOH A2033 1555 1555 1.98 LINK MG MG A 703 O HOH A2043 1555 1555 2.19 LINK MG MG A 704 O HOH A2006 1555 1555 2.51 LINK MG MG A 704 O HOH A2039 1555 1555 2.73 LINK OD1 ASP B 195 MG MG B 704 1555 1555 2.25 LINK OD1 ASP B 196 MG MG B 704 1555 1555 2.30 LINK O2G ANP B 702 MG MG B 703 1555 1555 1.93 LINK O1B ANP B 702 MG MG B 703 1555 1555 2.07 LINK O2A ANP B 702 MG MG B 703 1555 1555 1.90 LINK O1A ANP B 702 MG MG B 704 1555 1555 2.51 LINK O1G ANP B 702 MG MG B 704 1555 1555 2.31 LINK O3A ANP B 702 MG MG B 704 1555 1555 2.92 LINK MG MG B 703 O HOH B2006 1555 1555 1.95 LINK MG MG B 703 O HOH B2019 1555 1555 2.16 LINK MG MG B 703 O HOH B2029 1555 1555 1.92 LINK MG MG B 704 O HOH B2005 1555 1555 2.51 LINK MG MG B 704 O HOH B2025 1555 1555 2.79 SITE 1 AC1 11 ARG A 170 ILE A 171 SER A 194 ASP A 196 SITE 2 AC1 11 TYR A 199 TYR A 211 ARG A 213 ANP A 702 SITE 3 AC1 11 HOH A2032 HOH A2039 HOH A2042 SITE 1 AC2 30 HIS A 26 SER A 28 GLY A 29 GLU A 31 SITE 2 AC2 30 LYS A 49 HIS A 53 VAL A 122 ARG A 123 SITE 3 AC2 30 GLY A 124 ALA A 125 VAL A 144 ARG A 145 SITE 4 AC2 30 VAL A 146 LEU A 177 SER A 194 ASP A 195 SITE 5 AC2 30 ASP A 196 ARG A 227 PML A 701 MG A 703 SITE 6 AC2 30 MG A 704 HOH A2006 HOH A2007 HOH A2012 SITE 7 AC2 30 HOH A2025 HOH A2026 HOH A2033 HOH A2039 SITE 8 AC2 30 HOH A2042 HOH A2043 SITE 1 AC3 4 ANP A 702 HOH A2007 HOH A2033 HOH A2043 SITE 1 AC4 5 ASP A 195 ASP A 196 ANP A 702 HOH A2006 SITE 2 AC4 5 HOH A2039 SITE 1 AC5 12 ARG B 170 ILE B 171 SER B 194 ASP B 196 SITE 2 AC5 12 TYR B 199 THR B 201 TYR B 211 ARG B 213 SITE 3 AC5 12 ANP B 702 HOH B2018 HOH B2025 HOH B2028 SITE 1 AC6 29 HIS B 26 SER B 28 GLY B 29 GLU B 31 SITE 2 AC6 29 LYS B 49 HIS B 53 VAL B 122 ARG B 123 SITE 3 AC6 29 GLY B 124 ALA B 125 VAL B 144 ARG B 145 SITE 4 AC6 29 VAL B 146 LEU B 177 SER B 194 ASP B 195 SITE 5 AC6 29 ASP B 196 ARG B 227 PML B 701 MG B 703 SITE 6 AC6 29 MG B 704 HOH B2005 HOH B2006 HOH B2010 SITE 7 AC6 29 HOH B2014 HOH B2019 HOH B2025 HOH B2028 SITE 8 AC6 29 HOH B2029 SITE 1 AC7 4 ANP B 702 HOH B2006 HOH B2019 HOH B2029 SITE 1 AC8 5 ASP B 195 ASP B 196 ANP B 702 HOH B2005 SITE 2 AC8 5 HOH B2025 CRYST1 49.590 77.900 166.000 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 0.020165 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012837 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006024 0.00000 MTRIX1 1 0.310100 -0.944000 0.112900 18.11040 1 MTRIX2 1 -0.946200 -0.318000 -0.060500 44.27700 1 MTRIX3 1 0.093000 -0.088000 -0.991800 187.71880 1