HEADER LIGASE 04-SEP-12 4GXR TITLE STRUCTURE OF ATP BOUND RPMATB-BXBCLM CHIMERA B3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALONYL COA SYNTHETASE, BENZOATE-COA LIGASE CHIMERIC COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP Q6ND88 RESIDUES 1-443,455-503 AND UNP Q13WK3 473-483; COMPND 6 EC: 6.2.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS, BURKHOLDERIA SOURCE 3 XENOVORANS; SOURCE 4 ORGANISM_TAXID: 258594, 266265; SOURCE 5 STRAIN: CGA009; SOURCE 6 GENE: MATB, RPA0221; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: JE9314; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PTEV5 KEYWDS RPMATB-BXBCLM CHIMERA, ANL-SUPERFAMILY, METHYLMALONATE-COA LIGASE, KEYWDS 2 MALONATE-COA LIGASE, COA, METHYLMALONATE, MALONATE, ACETYLATION OF KEYWDS 3 K488 BY RPPAT, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR K.C.RANK,H.A.CROSBY,J.C.ESCALANTE-SEMERENA,I.RAYMENT REVDAT 4 13-SEP-23 4GXR 1 REMARK SEQADV LINK REVDAT 3 26-JUL-17 4GXR 1 SOURCE REMARK REVDAT 2 19-DEC-12 4GXR 1 JRNL REVDAT 1 24-OCT-12 4GXR 0 JRNL AUTH H.A.CROSBY,K.C.RANK,I.RAYMENT,J.C.ESCALANTE-SEMERENA JRNL TITL STRUCTURAL INSIGHTS INTO THE SUBSTRATE SPECIFICITY OF THE JRNL TITL 2 RHODOPSEUDOMONAS PALUSTRIS PROTEIN ACETYLTRANSFERASE RPPAT: JRNL TITL 3 IDENTIFICATION OF A LOOP CRITICAL FOR RECOGNITION BY RPPAT. JRNL REF J.BIOL.CHEM. V. 287 41392 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 23076154 JRNL DOI 10.1074/JBC.M112.417360 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 52933 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2833 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3782 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.1700 REMARK 3 BIN FREE R VALUE SET COUNT : 203 REMARK 3 BIN FREE R VALUE : 0.1890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3897 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 533 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.23000 REMARK 3 B12 (A**2) : -0.07000 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): 0.110 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.081 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4109 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3985 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5597 ; 1.169 ; 2.025 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9152 ; 0.697 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 521 ; 5.218 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;32.449 ;23.077 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 554 ;11.957 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;14.727 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 654 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4557 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 900 ; 0.001 ; 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 400 REMARK 3 ORIGIN FOR THE GROUP (A): -49.9808 5.8418 2.5156 REMARK 3 T TENSOR REMARK 3 T11: 0.0742 T22: 0.1222 REMARK 3 T33: 0.0807 T12: 0.0012 REMARK 3 T13: -0.0131 T23: 0.0668 REMARK 3 L TENSOR REMARK 3 L11: 0.4344 L22: 0.7201 REMARK 3 L33: 0.2201 L12: 0.1402 REMARK 3 L13: 0.1231 L23: 0.0257 REMARK 3 S TENSOR REMARK 3 S11: 0.0564 S12: 0.0132 S13: 0.0287 REMARK 3 S21: -0.0205 S22: -0.0354 S23: -0.0007 REMARK 3 S31: 0.0102 S32: -0.0604 S33: -0.0209 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 401 A 503 REMARK 3 ORIGIN FOR THE GROUP (A): -79.1010 -4.4448 -1.7336 REMARK 3 T TENSOR REMARK 3 T11: 0.0293 T22: 0.2295 REMARK 3 T33: 0.1004 T12: -0.0543 REMARK 3 T13: -0.0171 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 2.3807 L22: 1.9759 REMARK 3 L33: 1.8184 L12: -0.5995 REMARK 3 L13: 0.0556 L23: 0.0744 REMARK 3 S TENSOR REMARK 3 S11: 0.0099 S12: -0.0391 S13: -0.1928 REMARK 3 S21: -0.0434 S22: -0.0806 S23: 0.1956 REMARK 3 S31: 0.1094 S32: -0.3294 S33: 0.0706 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 4 REMARK 4 4GXR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074765. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK HIGH-RESOLUTION REMARK 200 DOUBLE-CRYSTAL MONOCHROMATOR. REMARK 200 LN2 COOLED FIRST CRYSTAL, REMARK 200 SAGITTAL FOCUSING 2ND CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.05800 REMARK 200 R SYM FOR SHELL (I) : 0.04800 REMARK 200 FOR SHELL : 6.086 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: PDB ENTRY 4FUT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIETHANOLAMINE (100 MM, PH 8.0), WITH REMARK 280 MAGNESIUM SULFATE (50 MM), MONOMETHYL POLYETHYLENE GLYCOL 5000 REMARK 280 (21 %, W/V), AND GLYCEROL (4 %, W/V), VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 15.97933 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 31.95867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.96900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.94833 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 7.98967 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 O1 CO3 A 608 O HOH A 842 2.04 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 SER A 277 -15.13 83.62 REMARK 500 ASN A 306 -147.43 49.05 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 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 601 O1B REMARK 620 2 ATP A 601 O1G 91.0 REMARK 620 3 HOH A1147 O 93.3 98.5 REMARK 620 4 HOH A1148 O 177.1 91.3 84.7 REMARK 620 5 HOH A1149 O 87.7 168.0 93.5 90.4 REMARK 620 6 HOH A1194 O 93.5 88.0 170.5 88.3 80.2 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 ATP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 A 608 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FUT RELATED DB: PDB REMARK 900 ATP BOUND RPMATB REMARK 900 RELATED ID: 4FUQ RELATED DB: PDB REMARK 900 APO RPMATB REMARK 900 RELATED ID: 2V7B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF A BENZOATE COA LIGASE FROM BURKHOLDERIA REMARK 900 XENOVORANS LB400 REMARK 900 RELATED ID: 4GXQ RELATED DB: PDB REMARK 900 ATP BOUND RPMATB-BXBCLM CHIMERA B1 REMARK 900 RELATED ID: 3NYR RELATED DB: PDB REMARK 900 MALONYL-COA AND AMP BOUND SCMATB REMARK 900 RELATED ID: 3NYQ RELATED DB: PDB REMARK 900 METHYLMALONYL-COA AND AMP BOUND SCMATB DBREF 4GXR A 1 443 UNP Q6ND88 Q6ND88_RHOPA 1 443 DBREF 4GXR A 444 454 UNP Q13WK3 Q13WK3_BURXL 473 483 DBREF 4GXR A 455 503 UNP Q6ND88 Q6ND88_RHOPA 455 503 SEQADV 4GXR ALA A 488 UNP Q6ND88 LYS 488 ENGINEERED MUTATION SEQRES 1 A 503 MET ASN ALA ASN LEU PHE ALA ARG LEU PHE ASP MLY LEU SEQRES 2 A 503 ASP ASP PRO HIS MLY LEU ALA ILE GLU THR ALA ALA GLY SEQRES 3 A 503 ASP MLY ILE SER TYR ALA GLU LEU VAL ALA ARG ALA GLY SEQRES 4 A 503 ARG VAL ALA ASN VAL LEU VAL ALA ARG GLY LEU GLN VAL SEQRES 5 A 503 GLY ASP ARG VAL ALA ALA GLN THR GLU MLY SER VAL GLU SEQRES 6 A 503 ALA LEU VAL LEU TYR LEU ALA THR VAL ARG ALA GLY GLY SEQRES 7 A 503 VAL TYR LEU PRO LEU ASN THR ALA TYR THR LEU HIS GLU SEQRES 8 A 503 LEU ASP TYR PHE ILE THR ASP ALA GLU PRO MLY ILE VAL SEQRES 9 A 503 VAL CYS ASP PRO SER MLY ARG ASP GLY ILE ALA ALA ILE SEQRES 10 A 503 ALA ALA MLY VAL GLY ALA THR VAL GLU THR LEU GLY PRO SEQRES 11 A 503 ASP GLY ARG GLY SER LEU THR ASP ALA ALA ALA GLY ALA SEQRES 12 A 503 SER GLU ALA PHE ALA THR ILE ASP ARG GLY ALA ASP ASP SEQRES 13 A 503 LEU ALA ALA ILE LEU TYR THR SER GLY THR THR GLY ARG SEQRES 14 A 503 SER MLY GLY ALA MET LEU SER HIS ASP ASN LEU ALA SER SEQRES 15 A 503 ASN SER LEU THR LEU VAL ASP TYR TRP ARG PHE THR PRO SEQRES 16 A 503 ASP ASP VAL LEU ILE HIS ALA LEU PRO ILE TYR HIS THR SEQRES 17 A 503 HIS GLY LEU PHE VAL ALA SER ASN VAL THR LEU PHE ALA SEQRES 18 A 503 ARG GLY SER MET ILE PHE LEU PRO MLY PHE ASP PRO ASP SEQRES 19 A 503 MLY ILE LEU ASP LEU MET ALA ARG ALA THR VAL LEU MET SEQRES 20 A 503 GLY VAL PRO THR PHE TYR THR ARG LEU LEU GLN SER PRO SEQRES 21 A 503 ARG LEU THR MLY GLU THR THR GLY HIS MET ARG LEU PHE SEQRES 22 A 503 ILE SER GLY SER ALA PRO LEU LEU ALA ASP THR HIS ARG SEQRES 23 A 503 GLU TRP SER ALA MLY THR GLY HIS ALA VAL LEU GLU ARG SEQRES 24 A 503 TYR GLY MET THR GLU THR ASN MET ASN THR SER ASN PRO SEQRES 25 A 503 TYR ASP GLY ASP ARG VAL PRO GLY ALA VAL GLY PRO ALA SEQRES 26 A 503 LEU PRO GLY VAL SER ALA ARG VAL THR ASP PRO GLU THR SEQRES 27 A 503 GLY MLY GLU LEU PRO ARG GLY ASP ILE GLY MET ILE GLU SEQRES 28 A 503 VAL MLY GLY PRO ASN VAL PHE MLY GLY TYR TRP ARG MET SEQRES 29 A 503 PRO GLU MLY THR MLY SER GLU PHE ARG ASP ASP GLY PHE SEQRES 30 A 503 PHE ILE THR GLY ASP LEU GLY MLY ILE ASP GLU ARG GLY SEQRES 31 A 503 TYR VAL HIS ILE LEU GLY ARG GLY MLY ASP LEU VAL ILE SEQRES 32 A 503 THR GLY GLY PHE ASN VAL TYR PRO MLY GLU ILE GLU SER SEQRES 33 A 503 GLU ILE ASP ALA MET PRO GLY VAL VAL GLU SER ALA VAL SEQRES 34 A 503 ILE GLY VAL PRO HIS ALA ASP PHE GLY GLU GLY VAL THR SEQRES 35 A 503 ALA PHE VAL VAL LEU MLY ARG GLU PHE ALA PRO SER GLU SEQRES 36 A 503 ALA GLN VAL LEU HIS GLY LEU ASP GLY GLN LEU ALA MLY SEQRES 37 A 503 PHE MLY MET PRO MLY MLY VAL ILE PHE VAL ASP ASP LEU SEQRES 38 A 503 PRO ARG ASN THR MET GLY ALA VAL GLN MLY ASN VAL LEU SEQRES 39 A 503 ARG GLU THR TYR MLY ASP ILE TYR MLY MODRES 4GXR MLY A 12 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 18 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 28 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 62 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 102 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 110 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 120 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 171 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 230 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 235 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 264 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 291 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 340 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 353 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 359 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 367 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 369 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 385 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 399 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 412 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 448 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 468 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 470 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 473 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 474 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 491 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 499 LYS N-DIMETHYL-LYSINE MODRES 4GXR MLY A 503 LYS N-DIMETHYL-LYSINE HET MLY A 12 11 HET MLY A 18 11 HET MLY A 28 11 HET MLY A 62 11 HET MLY A 102 11 HET MLY A 110 11 HET MLY A 120 11 HET MLY A 171 11 HET MLY A 230 11 HET MLY A 235 11 HET MLY A 264 11 HET MLY A 291 11 HET MLY A 340 11 HET MLY A 353 11 HET MLY A 359 11 HET MLY A 367 11 HET MLY A 369 11 HET MLY A 385 11 HET MLY A 399 11 HET MLY A 412 11 HET MLY A 448 11 HET MLY A 468 11 HET MLY A 470 11 HET MLY A 473 11 HET MLY A 474 11 HET MLY A 491 11 HET MLY A 499 11 HET MLY A 503 12 HET ATP A 601 31 HET MG A 602 1 HET GOL A 603 6 HET SO4 A 604 5 HET GOL A 605 6 HET GOL A 606 6 HET GOL A 607 6 HET CO3 A 608 4 HETNAM MLY N-DIMETHYL-LYSINE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM CO3 CARBONATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MLY 28(C8 H18 N2 O2) FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 MG MG 2+ FORMUL 4 GOL 4(C3 H8 O3) FORMUL 5 SO4 O4 S 2- FORMUL 9 CO3 C O3 2- FORMUL 10 HOH *533(H2 O) HELIX 1 1 ASN A 4 ASP A 11 1 8 HELIX 2 2 TYR A 31 ARG A 48 1 18 HELIX 3 3 SER A 63 ALA A 76 1 14 HELIX 4 4 THR A 88 GLU A 100 1 13 HELIX 5 5 MLY A 110 MLY A 120 1 11 HELIX 6 6 GLY A 134 GLY A 142 1 9 HELIX 7 7 HIS A 177 TRP A 191 1 15 HELIX 8 8 HIS A 207 PHE A 212 1 6 HELIX 9 9 PHE A 212 ARG A 222 1 11 HELIX 10 10 ASP A 232 MET A 240 1 9 HELIX 11 11 ALA A 241 ALA A 243 5 3 HELIX 12 12 VAL A 249 LEU A 257 1 9 HELIX 13 13 THR A 263 GLY A 268 1 6 HELIX 14 14 LEU A 281 GLY A 293 1 13 HELIX 15 15 MET A 364 GLU A 371 1 8 HELIX 16 16 MLY A 399 LEU A 401 5 3 HELIX 17 17 TYR A 410 ALA A 420 1 11 HELIX 18 18 SER A 454 GLY A 464 1 11 HELIX 19 19 ALA A 467 MET A 471 5 5 HELIX 20 20 GLN A 490 TYR A 498 1 9 SHEET 1 A 8 MLY A 28 SER A 30 0 SHEET 2 A 8 LEU A 19 THR A 23 -1 N ILE A 21 O ILE A 29 SHEET 3 A 8 SER A 224 PHE A 227 1 O PHE A 227 N GLU A 22 SHEET 4 A 8 VAL A 198 HIS A 201 1 N LEU A 199 O ILE A 226 SHEET 5 A 8 VAL A 245 GLY A 248 1 O VAL A 245 N ILE A 200 SHEET 6 A 8 LEU A 272 SER A 275 1 O ILE A 274 N LEU A 246 SHEET 7 A 8 LEU A 297 MET A 302 1 O LEU A 297 N PHE A 273 SHEET 8 A 8 ASN A 306 SER A 310 -1 O ASN A 308 N TYR A 300 SHEET 1 B 4 VAL A 79 PRO A 82 0 SHEET 2 B 4 ARG A 55 GLN A 59 1 N VAL A 56 O LEU A 81 SHEET 3 B 4 ILE A 103 CYS A 106 1 O VAL A 105 N ALA A 57 SHEET 4 B 4 THR A 124 THR A 127 1 O THR A 124 N VAL A 104 SHEET 1 C 2 LEU A 157 TYR A 162 0 SHEET 2 C 2 GLY A 172 SER A 176 -1 O ALA A 173 N LEU A 161 SHEET 1 D 4 SER A 330 THR A 334 0 SHEET 2 D 4 GLY A 348 MLY A 353 -1 O MLY A 353 N SER A 330 SHEET 3 D 4 PHE A 378 ILE A 386 -1 O PHE A 378 N VAL A 352 SHEET 4 D 4 VAL A 392 ARG A 397 -1 O GLY A 396 N LEU A 383 SHEET 1 E 2 VAL A 402 THR A 404 0 SHEET 2 E 2 PHE A 407 VAL A 409 -1 O VAL A 409 N VAL A 402 SHEET 1 F 3 VAL A 424 HIS A 434 0 SHEET 2 F 3 GLY A 438 LEU A 447 -1 O VAL A 446 N GLU A 426 SHEET 3 F 3 MLY A 474 PHE A 477 1 O ILE A 476 N ALA A 443 LINK C ASP A 11 N MLY A 12 1555 1555 1.33 LINK C MLY A 12 N LEU A 13 1555 1555 1.33 LINK C HIS A 17 N MLY A 18 1555 1555 1.33 LINK C MLY A 18 N LEU A 19 1555 1555 1.33 LINK C ASP A 27 N MLY A 28 1555 1555 1.33 LINK C MLY A 28 N ILE A 29 1555 1555 1.33 LINK C GLU A 61 N MLY A 62 1555 1555 1.32 LINK C MLY A 62 N SER A 63 1555 1555 1.33 LINK C PRO A 101 N MLY A 102 1555 1555 1.33 LINK C MLY A 102 N ILE A 103 1555 1555 1.33 LINK C SER A 109 N MLY A 110 1555 1555 1.33 LINK C MLY A 110 N ARG A 111 1555 1555 1.33 LINK C ALA A 119 N MLY A 120 1555 1555 1.33 LINK C MLY A 120 N VAL A 121 1555 1555 1.33 LINK C SER A 170 N MLY A 171 1555 1555 1.34 LINK C MLY A 171 N GLY A 172 1555 1555 1.33 LINK C PRO A 229 N MLY A 230 1555 1555 1.33 LINK C MLY A 230 N PHE A 231 1555 1555 1.33 LINK C ASP A 234 N MLY A 235 1555 1555 1.33 LINK C MLY A 235 N ILE A 236 1555 1555 1.33 LINK C THR A 263 N MLY A 264 1555 1555 1.33 LINK C MLY A 264 N GLU A 265 1555 1555 1.33 LINK C ALA A 290 N MLY A 291 1555 1555 1.33 LINK C MLY A 291 N THR A 292 1555 1555 1.34 LINK C GLY A 339 N MLY A 340 1555 1555 1.33 LINK C MLY A 340 N GLU A 341 1555 1555 1.33 LINK C VAL A 352 N MLY A 353 1555 1555 1.33 LINK C MLY A 353 N GLY A 354 1555 1555 1.33 LINK C PHE A 358 N MLY A 359 1555 1555 1.33 LINK C MLY A 359 N GLY A 360 1555 1555 1.33 LINK C GLU A 366 N MLY A 367 1555 1555 1.33 LINK C MLY A 367 N THR A 368 1555 1555 1.33 LINK C THR A 368 N MLY A 369 1555 1555 1.33 LINK C MLY A 369 N ASER A 370 1555 1555 1.33 LINK C MLY A 369 N BSER A 370 1555 1555 1.33 LINK C GLY A 384 N MLY A 385 1555 1555 1.33 LINK C MLY A 385 N ILE A 386 1555 1555 1.33 LINK C GLY A 398 N MLY A 399 1555 1555 1.33 LINK C MLY A 399 N ASP A 400 1555 1555 1.33 LINK C PRO A 411 N MLY A 412 1555 1555 1.34 LINK C MLY A 412 N GLU A 413 1555 1555 1.33 LINK C LEU A 447 N MLY A 448 1555 1555 1.33 LINK C MLY A 448 N ARG A 449 1555 1555 1.33 LINK C ALA A 467 N MLY A 468 1555 1555 1.33 LINK C MLY A 468 N PHE A 469 1555 1555 1.33 LINK C PHE A 469 N MLY A 470 1555 1555 1.33 LINK C MLY A 470 N MET A 471 1555 1555 1.33 LINK C PRO A 472 N MLY A 473 1555 1555 1.33 LINK C MLY A 473 N MLY A 474 1555 1555 1.33 LINK C MLY A 474 N VAL A 475 1555 1555 1.34 LINK C GLN A 490 N MLY A 491 1555 1555 1.33 LINK C MLY A 491 N ASN A 492 1555 1555 1.34 LINK C TYR A 498 N MLY A 499 1555 1555 1.33 LINK C MLY A 499 N ASP A 500 1555 1555 1.33 LINK C TYR A 502 N MLY A 503 1555 1555 1.33 LINK O1B ATP A 601 MG MG A 602 1555 1555 1.88 LINK O1G ATP A 601 MG MG A 602 1555 1555 1.95 LINK MG MG A 602 O HOH A1147 1555 1555 2.12 LINK MG MG A 602 O HOH A1148 1555 1555 2.07 LINK MG MG A 602 O HOH A1149 1555 1555 2.18 LINK MG MG A 602 O HOH A1194 1555 1555 2.25 SITE 1 AC1 29 THR A 163 SER A 164 GLY A 165 THR A 166 SITE 2 AC1 29 THR A 167 MLY A 171 HIS A 207 SER A 277 SITE 3 AC1 29 ALA A 278 PRO A 279 GLU A 298 ARG A 299 SITE 4 AC1 29 GLY A 301 MET A 302 THR A 303 VAL A 322 SITE 5 AC1 29 ASP A 382 ARG A 397 MG A 602 HOH A 827 SITE 6 AC1 29 HOH A 842 HOH A 891 HOH A1013 HOH A1028 SITE 7 AC1 29 HOH A1045 HOH A1147 HOH A1148 HOH A1149 SITE 8 AC1 29 HOH A1194 SITE 1 AC2 5 ATP A 601 HOH A1147 HOH A1148 HOH A1149 SITE 2 AC2 5 HOH A1194 SITE 1 AC3 3 ARG A 8 HOH A 876 HOH A1043 SITE 1 AC4 8 ASP A 283 ASP A 419 VAL A 424 VAL A 425 SITE 2 AC4 8 HOH A 965 HOH A1137 HOH A1200 HOH A1201 SITE 1 AC5 3 VAL A 52 ARG A 152 HOH A 908 SITE 1 AC6 6 PHE A 231 THR A 251 ARG A 255 THR A 485 SITE 2 AC6 6 GLY A 487 HOH A1207 SITE 1 AC7 7 ARG A 111 MLY A 264 ALA A 290 GLY A 293 SITE 2 AC7 7 HOH A 751 HOH A1012 HOH A1020 SITE 1 AC8 9 HIS A 207 THR A 208 HIS A 209 SER A 277 SITE 2 AC8 9 ARG A 299 GLY A 301 MET A 307 HOH A 842 SITE 3 AC8 9 HOH A 963 CRYST1 173.155 173.155 47.938 90.00 90.00 120.00 P 61 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 0.005775 0.003334 0.000000 0.00000 SCALE2 0.000000 0.006669 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020860 0.00000