HEADER TRANSFERASE 16-JUL-08 3DU4 TITLE CRYSTAL STRUCTURE OF 7-KETO-8-AMINOPELARGONIC ACID BOUND 7,8- TITLE 2 DIAMINOPELARGONIC ACID SYNTHASE IN BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 7,8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE, DAPA COMPND 5 AMINOTRANSFERASE; COMPND 6 EC: 2.6.1.62; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: BIOA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS AMINOTRANSFERASE, BIOTIN BIOSYNTHESIS, PYRIDOXAL PHOSPHATE, S- KEYWDS 2 ADENOSYL-L-METHIONINE, 7-KETO, 8-AMINO PELARGONIC ACID, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.DEY,J.C.SACCHETTINI REVDAT 4 30-AUG-23 3DU4 1 REMARK LINK REVDAT 3 13-JUL-11 3DU4 1 VERSN REVDAT 2 25-AUG-10 3DU4 1 JRNL REVDAT 1 23-JUN-09 3DU4 0 JRNL AUTH S.DEY,J.M.LANE,R.E.LEE,E.J.RUBIN,J.C.SACCHETTINI JRNL TITL STRUCTURAL CHARACTERIZATION OF THE MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS BIOTIN BIOSYNTHESIS ENZYMES JRNL TITL 3 7,8-DIAMINOPELARGONIC ACID SYNTHASE AND DETHIOBIOTIN JRNL TITL 4 SYNTHETASE . JRNL REF BIOCHEMISTRY V. 49 6746 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20565114 JRNL DOI 10.1021/BI902097J REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 41433 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2200 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2880 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7038 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 261 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.43000 REMARK 3 B22 (A**2) : 1.27000 REMARK 3 B33 (A**2) : -1.70000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.353 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.246 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.186 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.311 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7246 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9778 ; 1.434 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 894 ; NULL ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 316 ; NULL ;24.810 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1294 ; NULL ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ; NULL ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1070 ; NULL ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5402 ; NULL ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3645 ; NULL ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4881 ; NULL ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 659 ; NULL ; 0.500 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): 31 ; NULL ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; NULL ; 0.500 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): 4558 ; NULL ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7158 ; NULL ; 7.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3010 ; NULL ; 9.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2620 ; NULL ;11.000 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 : NULL 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: NULL REMARK 4 REMARK 4 3DU4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.5 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43651 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 72.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.220 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.48 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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 3DOD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M SODIUM THIOCYANATE, REMARK 280 5% XYLITOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 52.56650 REMARK 290 SMTRY3 2 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: 13130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 55 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 PHE A 171 CB - CA - C ANGL. DEV. = 12.5 DEGREES 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 75 -63.50 -120.68 REMARK 500 ILE A 76 146.43 -172.06 REMARK 500 PRO A 101 134.43 -39.13 REMARK 500 LYS A 143 130.35 -27.43 REMARK 500 PHE A 171 88.55 43.12 REMARK 500 SER A 186 -89.72 -69.47 REMARK 500 ASP A 188 88.28 53.94 REMARK 500 ARG A 193 -65.51 -28.44 REMARK 500 MET A 219 -33.24 70.45 REMARK 500 LYS A 280 -94.92 38.22 REMARK 500 ASP A 304 167.34 178.10 REMARK 500 ASN A 321 123.60 -35.38 REMARK 500 ASN A 339 52.29 31.99 REMARK 500 LYS A 385 24.71 49.52 REMARK 500 ASP A 391 -9.15 -59.50 REMARK 500 PRO A 421 151.42 -49.42 REMARK 500 VAL B 53 49.43 75.45 REMARK 500 ARG B 61 51.97 36.93 REMARK 500 LYS B 75 -62.68 -120.72 REMARK 500 ILE B 76 134.80 -173.42 REMARK 500 SER B 110 -162.89 -162.33 REMARK 500 SER B 158 53.32 -148.55 REMARK 500 SER B 184 -144.70 -87.09 REMARK 500 GLU B 185 -45.07 -140.83 REMARK 500 MET B 219 -37.65 80.10 REMARK 500 PHE B 257 64.06 61.70 REMARK 500 LYS B 280 -99.55 40.77 REMARK 500 THR B 319 122.37 -38.32 REMARK 500 ASN B 321 116.65 -39.47 REMARK 500 GLU B 383 -61.79 -23.51 REMARK 500 GLU B 447 44.63 29.85 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 HIS A 164 VAL A 165 142.55 REMARK 500 MET A 170 PHE A 171 57.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KAP A 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KAP B 451 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DOD RELATED DB: PDB REMARK 900 PLP-BOUND 7,8-DIAMINOPELARGONIC ACID SYNTHASE REMARK 900 RELATED ID: 3DRD RELATED DB: PDB REMARK 900 7,8-DIAMINO PELARGONIC ACID SYNTHASE APOENZYME DBREF 3DU4 A 1 448 UNP P53555 BIOA_BACSU 1 448 DBREF 3DU4 B 1 448 UNP P53555 BIOA_BACSU 1 448 SEQRES 1 A 448 MET THR HIS ASP LEU ILE GLU LYS SER LYS LYS HIS LEU SEQRES 2 A 448 TRP LEU PRO PHE THR GLN MET LYS ASP TYR ASP GLU ASN SEQRES 3 A 448 PRO LEU ILE ILE GLU SER GLY THR GLY ILE LYS VAL LYS SEQRES 4 A 448 ASP ILE ASN GLY LYS GLU TYR TYR ASP GLY PHE SER SER SEQRES 5 A 448 VAL TRP LEU ASN VAL HIS GLY HIS ARG LYS LYS GLU LEU SEQRES 6 A 448 ASP ASP ALA ILE LYS LYS GLN LEU GLY LYS ILE ALA HIS SEQRES 7 A 448 SER THR LEU LEU GLY MET THR ASN VAL PRO ALA THR GLN SEQRES 8 A 448 LEU ALA GLU THR LEU ILE ASP ILE SER PRO LYS LYS LEU SEQRES 9 A 448 THR ARG VAL PHE TYR SER ASP SER GLY ALA GLU ALA MET SEQRES 10 A 448 GLU ILE ALA LEU LYS MET ALA PHE GLN TYR TRP LYS ASN SEQRES 11 A 448 ILE GLY LYS PRO GLU LYS GLN LYS PHE ILE ALA MET LYS SEQRES 12 A 448 ASN GLY TYR HIS GLY ASP THR ILE GLY ALA VAL SER VAL SEQRES 13 A 448 GLY SER ILE GLU LEU PHE HIS HIS VAL TYR GLY PRO LEU SEQRES 14 A 448 MET PHE GLU SER TYR LYS ALA PRO ILE PRO TYR VAL TYR SEQRES 15 A 448 ARG SER GLU SER GLY ASP PRO ASP GLU CYS ARG ASP GLN SEQRES 16 A 448 CSX LEU ARG GLU LEU ALA GLN LEU LEU GLU GLU HIS HIS SEQRES 17 A 448 GLU GLU ILE ALA ALA LEU SER ILE GLU SER MET VAL GLN SEQRES 18 A 448 GLY ALA SER GLY MET ILE VAL MET PRO GLU GLY TYR LEU SEQRES 19 A 448 ALA GLY VAL ARG GLU LEU CYS THR THR TYR ASP VAL LEU SEQRES 20 A 448 MET ILE VAL ASP GLU VAL ALA THR GLY PHE GLY ARG THR SEQRES 21 A 448 GLY LYS MET PHE ALA CYS GLU HIS GLU ASN VAL GLN PRO SEQRES 22 A 448 ASP LEU MET ALA ALA GLY LYS GLY ILE THR GLY GLY TYR SEQRES 23 A 448 LEU PRO ILE ALA VAL THR PHE ALA THR GLU ASP ILE TYR SEQRES 24 A 448 LYS ALA PHE TYR ASP ASP TYR GLU ASN LEU LYS THR PHE SEQRES 25 A 448 PHE HIS GLY HIS SER TYR THR GLY ASN GLN LEU GLY CYS SEQRES 26 A 448 ALA VAL ALA LEU GLU ASN LEU ALA LEU PHE GLU SER GLU SEQRES 27 A 448 ASN ILE VAL GLU GLN VAL ALA GLU LYS SER LYS LYS LEU SEQRES 28 A 448 HIS PHE LEU LEU GLN ASP LEU HIS ALA LEU PRO HIS VAL SEQRES 29 A 448 GLY ASP ILE ARG GLN LEU GLY PHE MET CYS GLY ALA GLU SEQRES 30 A 448 LEU VAL ARG SER LYS GLU THR LYS GLU PRO TYR PRO ALA SEQRES 31 A 448 ASP ARG ARG ILE GLY TYR LYS VAL SER LEU LYS MET ARG SEQRES 32 A 448 GLU LEU GLY MET LEU THR ARG PRO LEU GLY ASP VAL ILE SEQRES 33 A 448 ALA PHE LEU PRO PRO LEU ALA SER THR ALA GLU GLU LEU SEQRES 34 A 448 SER GLU MET VAL ALA ILE MET LYS GLN ALA ILE HIS GLU SEQRES 35 A 448 VAL THR SER LEU GLU ASP SEQRES 1 B 448 MET THR HIS ASP LEU ILE GLU LYS SER LYS LYS HIS LEU SEQRES 2 B 448 TRP LEU PRO PHE THR GLN MET LYS ASP TYR ASP GLU ASN SEQRES 3 B 448 PRO LEU ILE ILE GLU SER GLY THR GLY ILE LYS VAL LYS SEQRES 4 B 448 ASP ILE ASN GLY LYS GLU TYR TYR ASP GLY PHE SER SER SEQRES 5 B 448 VAL TRP LEU ASN VAL HIS GLY HIS ARG LYS LYS GLU LEU SEQRES 6 B 448 ASP ASP ALA ILE LYS LYS GLN LEU GLY LYS ILE ALA HIS SEQRES 7 B 448 SER THR LEU LEU GLY MET THR ASN VAL PRO ALA THR GLN SEQRES 8 B 448 LEU ALA GLU THR LEU ILE ASP ILE SER PRO LYS LYS LEU SEQRES 9 B 448 THR ARG VAL PHE TYR SER ASP SER GLY ALA GLU ALA MET SEQRES 10 B 448 GLU ILE ALA LEU LYS MET ALA PHE GLN TYR TRP LYS ASN SEQRES 11 B 448 ILE GLY LYS PRO GLU LYS GLN LYS PHE ILE ALA MET LYS SEQRES 12 B 448 ASN GLY TYR HIS GLY ASP THR ILE GLY ALA VAL SER VAL SEQRES 13 B 448 GLY SER ILE GLU LEU PHE HIS HIS VAL TYR GLY PRO LEU SEQRES 14 B 448 MET PHE GLU SER TYR LYS ALA PRO ILE PRO TYR VAL TYR SEQRES 15 B 448 ARG SER GLU SER GLY ASP PRO ASP GLU CYS ARG ASP GLN SEQRES 16 B 448 CSX LEU ARG GLU LEU ALA GLN LEU LEU GLU GLU HIS HIS SEQRES 17 B 448 GLU GLU ILE ALA ALA LEU SER ILE GLU SER MET VAL GLN SEQRES 18 B 448 GLY ALA SER GLY MET ILE VAL MET PRO GLU GLY TYR LEU SEQRES 19 B 448 ALA GLY VAL ARG GLU LEU CYS THR THR TYR ASP VAL LEU SEQRES 20 B 448 MET ILE VAL ASP GLU VAL ALA THR GLY PHE GLY ARG THR SEQRES 21 B 448 GLY LYS MET PHE ALA CYS GLU HIS GLU ASN VAL GLN PRO SEQRES 22 B 448 ASP LEU MET ALA ALA GLY LYS GLY ILE THR GLY GLY TYR SEQRES 23 B 448 LEU PRO ILE ALA VAL THR PHE ALA THR GLU ASP ILE TYR SEQRES 24 B 448 LYS ALA PHE TYR ASP ASP TYR GLU ASN LEU LYS THR PHE SEQRES 25 B 448 PHE HIS GLY HIS SER TYR THR GLY ASN GLN LEU GLY CYS SEQRES 26 B 448 ALA VAL ALA LEU GLU ASN LEU ALA LEU PHE GLU SER GLU SEQRES 27 B 448 ASN ILE VAL GLU GLN VAL ALA GLU LYS SER LYS LYS LEU SEQRES 28 B 448 HIS PHE LEU LEU GLN ASP LEU HIS ALA LEU PRO HIS VAL SEQRES 29 B 448 GLY ASP ILE ARG GLN LEU GLY PHE MET CYS GLY ALA GLU SEQRES 30 B 448 LEU VAL ARG SER LYS GLU THR LYS GLU PRO TYR PRO ALA SEQRES 31 B 448 ASP ARG ARG ILE GLY TYR LYS VAL SER LEU LYS MET ARG SEQRES 32 B 448 GLU LEU GLY MET LEU THR ARG PRO LEU GLY ASP VAL ILE SEQRES 33 B 448 ALA PHE LEU PRO PRO LEU ALA SER THR ALA GLU GLU LEU SEQRES 34 B 448 SER GLU MET VAL ALA ILE MET LYS GLN ALA ILE HIS GLU SEQRES 35 B 448 VAL THR SER LEU GLU ASP MODRES 3DU4 CSX A 196 CYS S-OXY CYSTEINE MODRES 3DU4 CSX B 196 CYS S-OXY CYSTEINE HET CSX A 196 7 HET CSX B 196 7 HET PLP A 450 15 HET KAP A 451 13 HET PLP B 450 15 HET KAP B 451 13 HETNAM CSX S-OXY CYSTEINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM KAP 7-KETO-8-AMINOPELARGONIC ACID HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 1 CSX 2(C3 H7 N O3 S) FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 KAP 2(C9 H17 N O3) FORMUL 7 HOH *261(H2 O) HELIX 1 1 MET A 1 LEU A 13 1 13 HELIX 2 2 GLN A 19 ASN A 26 1 8 HELIX 3 3 PHE A 50 LEU A 55 1 6 HELIX 4 4 LYS A 62 GLY A 74 1 13 HELIX 5 5 VAL A 87 SER A 100 1 14 HELIX 6 6 SER A 112 ILE A 131 1 20 HELIX 7 7 THR A 150 VAL A 156 1 7 HELIX 8 8 TYR A 166 MET A 170 5 5 HELIX 9 9 ASP A 188 HIS A 208 1 21 HELIX 10 10 GLY A 232 TYR A 244 1 13 HELIX 11 11 PHE A 264 ASN A 270 5 7 HELIX 12 12 GLY A 279 GLY A 284 5 6 HELIX 13 13 GLU A 296 LYS A 300 1 5 HELIX 14 14 ALA A 301 TYR A 303 5 3 HELIX 15 15 ASN A 321 GLU A 338 1 18 HELIX 16 16 ASN A 339 HIS A 359 1 21 HELIX 17 17 PRO A 389 ARG A 392 5 4 HELIX 18 18 ARG A 393 LEU A 405 1 13 HELIX 19 19 THR A 425 SER A 445 1 21 HELIX 20 20 THR B 2 LEU B 13 1 12 HELIX 21 21 GLN B 19 ASN B 26 1 8 HELIX 22 22 PHE B 50 LEU B 55 1 6 HELIX 23 23 LYS B 62 GLY B 74 1 13 HELIX 24 24 VAL B 87 SER B 100 1 14 HELIX 25 25 SER B 112 ILE B 131 1 20 HELIX 26 26 THR B 150 SER B 155 1 6 HELIX 27 27 ILE B 159 HIS B 164 1 6 HELIX 28 28 VAL B 165 MET B 170 5 6 HELIX 29 29 ASP B 188 HIS B 208 1 21 HELIX 30 30 GLY B 232 TYR B 244 1 13 HELIX 31 31 PHE B 264 HIS B 268 5 5 HELIX 32 32 GLY B 279 GLY B 284 5 6 HELIX 33 33 THR B 295 ALA B 301 1 7 HELIX 34 34 ASP B 305 LEU B 309 5 5 HELIX 35 35 ASN B 321 ASN B 339 1 19 HELIX 36 36 ASN B 339 ASP B 357 1 19 HELIX 37 37 LEU B 358 LEU B 361 5 4 HELIX 38 38 PRO B 389 ARG B 392 5 4 HELIX 39 39 ARG B 393 LEU B 405 1 13 HELIX 40 40 THR B 425 SER B 445 1 21 SHEET 1 A 5 MET A 407 LEU A 408 0 SHEET 2 A 5 GLU A 45 ASP A 48 1 N TYR A 47 O LEU A 408 SHEET 3 A 5 LYS A 37 ASP A 40 -1 N VAL A 38 O TYR A 46 SHEET 4 A 5 ILE A 29 THR A 34 -1 N GLU A 31 O LYS A 39 SHEET 5 A 5 THR B 85 ASN B 86 1 O THR B 85 N ILE A 30 SHEET 1 B 5 THR A 85 ASN A 86 0 SHEET 2 B 5 ILE B 29 THR B 34 1 O ILE B 30 N THR A 85 SHEET 3 B 5 LYS B 37 ASP B 40 -1 O LYS B 39 N GLU B 31 SHEET 4 B 5 GLU B 45 ASP B 48 -1 O TYR B 46 N VAL B 38 SHEET 5 B 5 MET B 407 LEU B 408 1 O LEU B 408 N TYR B 47 SHEET 1 C 7 LEU A 104 SER A 110 0 SHEET 2 C 7 ALA A 290 THR A 295 -1 O ALA A 290 N SER A 110 SHEET 3 C 7 LEU A 275 ALA A 278 -1 N MET A 276 O PHE A 293 SHEET 4 C 7 LEU A 247 ASP A 251 1 N VAL A 250 O LEU A 275 SHEET 5 C 7 ILE A 211 GLU A 217 1 N LEU A 214 O ILE A 249 SHEET 6 C 7 LYS A 138 MET A 142 1 N ILE A 140 O SER A 215 SHEET 7 C 7 SER A 173 ALA A 176 1 O TYR A 174 N PHE A 139 SHEET 1 D 2 VAL A 220 GLN A 221 0 SHEET 2 D 2 ILE A 227 VAL A 228 -1 O ILE A 227 N GLN A 221 SHEET 1 E 4 VAL A 364 LEU A 370 0 SHEET 2 E 4 MET A 373 LEU A 378 -1 O GLY A 375 N ARG A 368 SHEET 3 E 4 VAL A 415 PHE A 418 -1 O PHE A 418 N CYS A 374 SHEET 4 E 4 PRO A 411 LEU A 412 -1 N LEU A 412 O VAL A 415 SHEET 1 F 7 ARG B 106 SER B 110 0 SHEET 2 F 7 ALA B 290 ALA B 294 -1 O THR B 292 N PHE B 108 SHEET 3 F 7 LEU B 275 ALA B 278 -1 N MET B 276 O PHE B 293 SHEET 4 F 7 LEU B 247 ASP B 251 1 N VAL B 250 O LEU B 275 SHEET 5 F 7 ILE B 211 GLU B 217 1 N LEU B 214 O ILE B 249 SHEET 6 F 7 LYS B 138 MET B 142 1 N ILE B 140 O SER B 215 SHEET 7 F 7 SER B 173 ALA B 176 1 O ALA B 176 N ALA B 141 SHEET 1 G 2 VAL B 220 GLN B 221 0 SHEET 2 G 2 ILE B 227 VAL B 228 -1 O ILE B 227 N GLN B 221 SHEET 1 H 4 VAL B 364 LEU B 370 0 SHEET 2 H 4 MET B 373 LEU B 378 -1 O GLU B 377 N GLY B 365 SHEET 3 H 4 VAL B 415 PHE B 418 -1 O PHE B 418 N CYS B 374 SHEET 4 H 4 PRO B 411 LEU B 412 -1 N LEU B 412 O VAL B 415 LINK C GLN A 195 N CSX A 196 1555 1555 1.33 LINK C CSX A 196 N LEU A 197 1555 1555 1.34 LINK NZ LYS A 280 C4A PLP A 450 1555 1555 1.27 LINK C GLN B 195 N CSX B 196 1555 1555 1.33 LINK C CSX B 196 N LEU B 197 1555 1555 1.34 LINK NZ LYS B 280 C4A PLP B 450 1555 1555 1.27 CISPEP 1 GLY A 187 ASP A 188 0 8.42 SITE 1 AC1 12 SER A 112 GLY A 113 ALA A 114 TYR A 146 SITE 2 AC1 12 HIS A 147 GLY A 148 GLU A 217 ASP A 251 SITE 3 AC1 12 ALA A 254 LYS A 280 HIS B 316 SER B 317 SITE 1 AC2 6 TYR A 146 ASP A 149 LYS A 280 ARG A 410 SITE 2 AC2 6 LEU B 82 GLY B 315 SITE 1 AC3 12 HIS A 316 SER A 317 SER B 112 GLY B 113 SITE 2 AC3 12 ALA B 114 TYR B 146 HIS B 147 GLY B 148 SITE 3 AC3 12 GLU B 217 ASP B 251 ALA B 254 LYS B 280 SITE 1 AC4 6 GLY A 315 PHE B 17 TYR B 146 ASP B 149 SITE 2 AC4 6 LYS B 280 ARG B 410 CRYST1 57.692 105.133 75.063 90.00 105.19 90.00 P 1 21 1 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 0.017334 0.000000 0.004705 0.00000 SCALE2 0.000000 0.009512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013804 0.00000