HEADER LIGASE 13-MAR-08 2VQD TITLE CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM PSEUDOMONAS AERUGINOSA TITLE 2 COMPLEXED WITH AMPCP COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIOTIN CARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACETYL-COA CARBOXYLASE SUBUNIT A, ACC; COMPND 5 EC: 6.3.4.14; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOTIDE-BINDING, FATTY ACID BIOSYNTHESIS, LIPID SYNTHESIS, ATP- KEYWDS 2 GRASP DOMAIN, BIOTIN CARBOXYLASE, LIGASE, BIOTIN, BACTERIA, ATP- KEYWDS 3 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR I.MOCHALKIN REVDAT 6 13-DEC-23 2VQD 1 LINK REVDAT 5 05-JUL-17 2VQD 1 REMARK REVDAT 4 13-JUL-11 2VQD 1 VERSN REVDAT 3 24-FEB-09 2VQD 1 VERSN REVDAT 2 30-SEP-08 2VQD 1 JRNL REVDAT 1 09-SEP-08 2VQD 0 JRNL AUTH I.MOCHALKIN,J.R.MILLER,A.EVDOKIMOV,S.LIGHTLE,C.YAN, JRNL AUTH 2 C.K.STOVER,G.L.WALDROP JRNL TITL STRUCTURAL EVIDENCE FOR SUBSTRATE-INDUCED SYNERGISM AND JRNL TITL 2 HALF-SITES REACTIVITY IN BIOTIN CARBOXYLASE. JRNL REF PROTEIN SCI. V. 17 1706 2008 JRNL REFN ISSN 0961-8368 JRNL PMID 18725455 JRNL DOI 10.1110/PS.035584.108 REMARK 2 REMARK 2 RESOLUTION. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 14953 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 791 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) : 2.41 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 884 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3412 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.51000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -1.73000 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): 1.859 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.311 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.229 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.358 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3514 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3247 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4756 ; 1.212 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7541 ; 0.758 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 448 ; 5.853 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 156 ;36.850 ;23.718 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 600 ;15.604 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;16.911 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 529 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3943 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 697 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 691 ; 0.188 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3225 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1687 ; 0.165 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2141 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 176 ; 0.149 ; 0.200 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): 17 ; 0.147 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 84 ; 0.182 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.172 ; 0.200 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): 2883 ; 0.543 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3558 ; 0.619 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1469 ; 1.021 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1198 ; 1.503 ; 4.500 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 447 REMARK 3 ORIGIN FOR THE GROUP (A): 6.1219 20.3449 13.0923 REMARK 3 T TENSOR REMARK 3 T11: -0.0552 T22: -0.0555 REMARK 3 T33: -0.0993 T12: -0.0093 REMARK 3 T13: -0.0309 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 0.5996 L22: 1.9352 REMARK 3 L33: 0.3516 L12: 0.0165 REMARK 3 L13: -0.1497 L23: -0.3972 REMARK 3 S TENSOR REMARK 3 S11: 0.0393 S12: 0.0107 S13: 0.0827 REMARK 3 S21: 0.2110 S22: -0.0420 S23: -0.1140 REMARK 3 S31: -0.0783 S32: -0.0012 S33: 0.0027 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 1448 A 1448 REMARK 3 ORIGIN FOR THE GROUP (A): 0.3358 31.0848 9.8703 REMARK 3 T TENSOR REMARK 3 T11: 0.0057 T22: 0.0004 REMARK 3 T33: 0.0031 T12: -0.0160 REMARK 3 T13: 0.0067 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 19.7093 L22: 30.0504 REMARK 3 L33: 14.9986 L12: -0.3605 REMARK 3 L13: 17.1687 L23: 0.8228 REMARK 3 S TENSOR REMARK 3 S11: 0.6192 S12: -0.5199 S13: 0.7931 REMARK 3 S21: -0.1356 S22: -0.8025 S23: 1.4562 REMARK 3 S31: -0.2469 S32: 0.4023 S33: 0.1833 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2VQD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1290035552. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15777 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1DV2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES (PH 7.0), 0.2M MGCL2, 15 REMARK 280 -20% PEG3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 32.11350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.39300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.11350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.39300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2176 LIES ON A SPECIAL POSITION. 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 LYS A 448 REMARK 465 HIS A 449 REMARK 465 GLY A 450 REMARK 465 SER A 451 REMARK 465 GLU A 452 REMARK 465 ASN A 453 REMARK 465 LEU A 454 REMARK 465 TYR A 455 REMARK 465 PHE A 456 REMARK 465 GLN A 457 REMARK 465 GLY A 458 REMARK 465 HIS A 459 REMARK 465 HIS A 460 REMARK 465 HIS A 461 REMARK 465 HIS A 462 REMARK 465 HIS A 463 REMARK 465 HIS A 464 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 ASN A 9 -168.39 -168.00 REMARK 500 PRO A 53 -174.39 -69.66 REMARK 500 SER A 59 -84.29 -136.11 REMARK 500 PHE A 84 -111.93 44.21 REMARK 500 ASN A 281 59.73 35.50 REMARK 500 THR A 291 58.37 -101.55 REMARK 500 TYR A 381 -169.28 -126.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 444 GLY A 445 38.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2013 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH A2019 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A2023 DISTANCE = 7.20 ANGSTROMS REMARK 525 HOH A2056 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A2074 DISTANCE = 6.45 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER (AP2): REMARK 600 NON-HYDROLYZABLE ADP ANALOG 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 A1449 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 276 OE1 REMARK 620 2 GLU A 288 OE2 78.2 REMARK 620 3 AP2 A1448 O2A 80.2 71.8 REMARK 620 4 AP2 A1448 O1B 153.8 91.2 73.7 REMARK 620 5 HOH A2133 O 83.6 159.3 95.6 101.1 REMARK 620 6 HOH A2139 O 93.3 80.3 152.0 108.5 110.9 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 AP2 A1448 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1449 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1450 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2C00 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM PSEUDOMONAS AERUGINOSA REMARK 900 IN APO FORM REMARK 900 RELATED ID: 2J9G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E. COLI IN COMPLEX REMARK 900 WITH AMPPNP AND ADP REMARK 900 RELATED ID: 2VPQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM S. AUREUS COMPLEXED REMARK 900 WITH AMPPNP REMARK 900 RELATED ID: 2VR1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E. COLI IN COMPLEX REMARK 900 WITH ATP ANALOG, ADPCF2P. REMARK 999 REMARK 999 SEQUENCE REMARK 999 C-TERMINAL HIS-TAG PRESENT DBREF 2VQD A 1 449 UNP P37798 ACCC_PSEAE 1 449 DBREF 2VQD A 450 464 PDB 2VQD 2VQD 450 464 SEQRES 1 A 464 MET LEU GLU LYS VAL LEU ILE ALA ASN ARG GLY GLU ILE SEQRES 2 A 464 ALA LEU ARG ILE LEU ARG ALA CYS LYS GLU LEU GLY ILE SEQRES 3 A 464 LYS THR VAL ALA VAL HIS SER THR ALA ASP ARG GLU LEU SEQRES 4 A 464 MET HIS LEU SER LEU ALA ASP GLU SER VAL CYS ILE GLY SEQRES 5 A 464 PRO ALA PRO ALA THR GLN SER TYR LEU GLN ILE PRO ALA SEQRES 6 A 464 ILE ILE ALA ALA ALA GLU VAL THR GLY ALA THR ALA ILE SEQRES 7 A 464 HIS PRO GLY TYR GLY PHE LEU ALA GLU ASN ALA ASP PHE SEQRES 8 A 464 ALA GLU GLN ILE GLU ARG SER GLY PHE THR PHE VAL GLY SEQRES 9 A 464 PRO THR ALA GLU VAL ILE ARG LEU MET GLY ASP LYS VAL SEQRES 10 A 464 SER ALA LYS ASP ALA MET LYS ARG ALA GLY VAL PRO THR SEQRES 11 A 464 VAL PRO GLY SER ASP GLY PRO LEU PRO GLU ASP GLU GLU SEQRES 12 A 464 THR ALA LEU ALA ILE ALA ARG GLU VAL GLY TYR PRO VAL SEQRES 13 A 464 ILE ILE LYS ALA ALA GLY GLY GLY GLY GLY ARG GLY MET SEQRES 14 A 464 ARG VAL VAL TYR ASP GLU SER GLU LEU ILE LYS SER ALA SEQRES 15 A 464 LYS LEU THR ARG THR GLU ALA GLY ALA ALA PHE GLY ASN SEQRES 16 A 464 PRO MET VAL TYR LEU GLU LYS PHE LEU THR ASN PRO ARG SEQRES 17 A 464 HIS VAL GLU VAL GLN VAL LEU SER ASP GLY GLN GLY ASN SEQRES 18 A 464 ALA ILE HIS LEU GLY ASP ARG ASP CYS SER LEU GLN ARG SEQRES 19 A 464 ARG HIS GLN LYS VAL ILE GLU GLU ALA PRO ALA PRO GLY SEQRES 20 A 464 ILE ASP GLU LYS ALA ARG GLN GLU VAL PHE ALA ARG CYS SEQRES 21 A 464 VAL GLN ALA CYS ILE GLU ILE GLY TYR ARG GLY ALA GLY SEQRES 22 A 464 THR PHE GLU PHE LEU TYR GLU ASN GLY ARG PHE TYR PHE SEQRES 23 A 464 ILE GLU MET ASN THR ARG VAL GLN VAL GLU HIS PRO VAL SEQRES 24 A 464 SER GLU MET VAL THR GLY VAL ASP ILE VAL LYS GLU MET SEQRES 25 A 464 LEU ARG ILE ALA SER GLY GLU LYS LEU SER ILE ARG GLN SEQRES 26 A 464 GLU ASP VAL VAL ILE ARG GLY HIS ALA LEU GLU CYS ARG SEQRES 27 A 464 ILE ASN ALA GLU ASP PRO LYS THR PHE MET PRO SER PRO SEQRES 28 A 464 GLY LYS VAL LYS HIS PHE HIS ALA PRO GLY GLY ASN GLY SEQRES 29 A 464 VAL ARG VAL ASP SER HIS LEU TYR SER GLY TYR SER VAL SEQRES 30 A 464 PRO PRO ASN TYR ASP SER LEU VAL GLY LYS VAL ILE THR SEQRES 31 A 464 TYR GLY ALA ASP ARG ASP GLU ALA LEU ALA ARG MET ARG SEQRES 32 A 464 ASN ALA LEU ASP GLU LEU ILE VAL ASP GLY ILE LYS THR SEQRES 33 A 464 ASN THR GLU LEU HIS LYS ASP LEU VAL ARG ASP ALA ALA SEQRES 34 A 464 PHE CYS LYS GLY GLY VAL ASN ILE HIS TYR LEU GLU LYS SEQRES 35 A 464 LYS LEU GLY MET ASP LYS HIS GLY SER GLU ASN LEU TYR SEQRES 36 A 464 PHE GLN GLY HIS HIS HIS HIS HIS HIS HET AP2 A1448 27 HET MG A1449 1 HET SO4 A1450 5 HETNAM AP2 PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 2 AP2 C11 H17 N5 O9 P2 FORMUL 3 MG MG 2+ FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *232(H2 O) HELIX 1 1 ARG A 10 LEU A 24 1 15 HELIX 2 2 ALA A 35 ARG A 37 5 3 HELIX 3 3 LEU A 39 ALA A 45 1 7 HELIX 4 4 PRO A 55 SER A 59 5 5 HELIX 5 5 GLN A 62 GLY A 74 1 13 HELIX 6 6 ASN A 88 SER A 98 1 11 HELIX 7 7 THR A 106 ASP A 115 1 10 HELIX 8 8 ASP A 115 ALA A 126 1 12 HELIX 9 9 ASP A 141 GLY A 153 1 13 HELIX 10 10 ASP A 174 SER A 176 5 3 HELIX 11 11 GLU A 177 GLY A 194 1 18 HELIX 12 12 ASP A 249 GLY A 268 1 20 HELIX 13 13 GLU A 296 GLY A 305 1 10 HELIX 14 14 ASP A 307 SER A 317 1 11 HELIX 15 15 ARG A 324 VAL A 328 5 5 HELIX 16 16 ASP A 394 LEU A 409 1 16 HELIX 17 17 ASN A 417 VAL A 425 1 9 HELIX 18 18 ASP A 427 GLY A 433 1 7 HELIX 19 19 HIS A 438 GLY A 445 1 8 SHEET 1 AA 5 GLU A 47 GLY A 52 0 SHEET 2 AA 5 LYS A 27 SER A 33 1 O THR A 28 N GLU A 47 SHEET 3 AA 5 LYS A 4 ILE A 7 1 O VAL A 5 N VAL A 29 SHEET 4 AA 5 ALA A 77 HIS A 79 1 O ALA A 77 N LEU A 6 SHEET 5 AA 5 THR A 101 PHE A 102 1 O THR A 101 N ILE A 78 SHEET 1 AB 3 MET A 169 VAL A 172 0 SHEET 2 AB 3 VAL A 156 ALA A 160 -1 O VAL A 156 N VAL A 172 SHEET 3 AB 3 VAL A 198 LYS A 202 -1 O TYR A 199 N LYS A 159 SHEET 1 AC 4 ALA A 222 ASP A 229 0 SHEET 2 AC 4 ARG A 208 ASP A 217 -1 O GLU A 211 N ARG A 228 SHEET 3 AC 4 ARG A 270 GLU A 280 -1 O GLY A 271 N SER A 216 SHEET 4 AC 4 ARG A 283 ASN A 290 -1 O ARG A 283 N GLU A 280 SHEET 1 AD 2 GLN A 233 ARG A 234 0 SHEET 2 AD 2 GLN A 237 LYS A 238 -1 O GLN A 237 N ARG A 234 SHEET 1 AE 4 ILE A 240 ALA A 243 0 SHEET 2 AE 4 HIS A 333 ASN A 340 -1 O ALA A 334 N ALA A 243 SHEET 3 AE 4 LEU A 384 GLY A 392 -1 N VAL A 385 O ILE A 339 SHEET 4 AE 4 VAL A 365 SER A 369 -1 O ARG A 366 N ILE A 389 SHEET 1 AF 2 GLY A 352 VAL A 354 0 SHEET 2 AF 2 TYR A 375 VAL A 377 -1 O TYR A 375 N VAL A 354 SHEET 1 AG 2 HIS A 356 HIS A 358 0 SHEET 2 AG 2 ILE A 410 ASP A 412 -1 O ILE A 410 N HIS A 358 LINK OE1 GLU A 276 MG MG A1449 1555 1555 2.36 LINK OE2 GLU A 288 MG MG A1449 1555 1555 1.89 LINK O2A AP2 A1448 MG MG A1449 1555 1555 2.37 LINK O1B AP2 A1448 MG MG A1449 1555 1555 2.01 LINK MG MG A1449 O HOH A2133 1555 1555 2.20 LINK MG MG A1449 O HOH A2139 1555 1555 2.00 CISPEP 1 TYR A 154 PRO A 155 0 2.46 CISPEP 2 ALA A 243 PRO A 244 0 -10.32 SITE 1 AC1 22 LYS A 116 ILE A 157 LYS A 159 GLY A 163 SITE 2 AC1 22 GLY A 164 GLY A 165 GLY A 166 MET A 169 SITE 3 AC1 22 GLU A 201 LYS A 202 PHE A 203 LEU A 204 SITE 4 AC1 22 HIS A 209 GLN A 233 HIS A 236 GLU A 276 SITE 5 AC1 22 LEU A 278 GLU A 288 ILE A 437 MG A1449 SITE 6 AC1 22 HOH A2092 HOH A2231 SITE 1 AC2 5 GLU A 276 GLU A 288 AP2 A1448 HOH A2133 SITE 2 AC2 5 HOH A2139 SITE 1 AC3 7 GLU A 87 MET A 113 GLY A 114 GLY A 163 SITE 2 AC3 7 GLU A 288 MET A 289 HOH A2140 CRYST1 64.227 126.786 49.878 90.00 90.00 90.00 P 21 21 2 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 0.015570 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020049 0.00000