HEADER LYASE 09-JAN-09 3FSJ TITLE CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE IN COMPLEX WITH THE TITLE 2 INHIBITOR MBP COMPND MOL_ID: 1; COMPND 2 MOLECULE: BENZOYLFORMATE DECARBOXYLASE; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: BFD, BFDC; COMPND 5 EC: 4.1.1.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 STRAIN: DSM 291 / NCIB 9494 / NCTC 10936 / STANIER 90; SOURCE 5 ATCC: 12633; SOURCE 6 GENE: MDLC; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS THIAMIN ADDUCT, AROMATIC HYDROCARBONS CATABOLISM, CALCIUM, KEYWDS 2 DECARBOXYLASE, LYASE, MAGNESIUM, MANDELATE PATHWAY, METAL BINDING, KEYWDS 3 THIAMINE PYROPHOSPHATE, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.S.BRANDT,G.L.KENYON,M.J.MCLEISH,F.JORDAN,G.A.PETSKO,D.RINGE REVDAT 3 06-SEP-23 3FSJ 1 REMARK LINK REVDAT 2 28-APR-09 3FSJ 1 JRNL REVDAT 1 27-JAN-09 3FSJ 0 JRNL AUTH G.S.BRANDT,M.M.KNEEN,S.CHAKRABORTY,A.T.BAYKAL,N.NEMERIA, JRNL AUTH 2 A.YEP,D.I.RUBY,G.A.PETSKO,G.L.KENYON,M.J.MCLEISH,F.JORDAN, JRNL AUTH 3 D.RINGE JRNL TITL SNAPSHOT OF A REACTION INTERMEDIATE: ANALYSIS OF JRNL TITL 2 BENZOYLFORMATE DECARBOXYLASE IN COMPLEX WITH A JRNL TITL 3 BENZOYLPHOSPHONATE INHIBITOR. JRNL REF BIOCHEMISTRY V. 48 3247 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19320438 JRNL DOI 10.1021/BI801950K REMARK 2 REMARK 2 RESOLUTION. 1.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 109983 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 11021 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) : 1.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7011 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 835 REMARK 3 BIN FREE R VALUE : 0.2240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3935 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 485 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -0.02000 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): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.052 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.027 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.635 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4077 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5582 ; 1.214 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 525 ; 5.773 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;34.082 ;24.419 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 601 ;11.731 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;12.556 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 621 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3158 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1965 ; 0.193 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2830 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 364 ; 0.103 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 6 ; 0.142 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 120 ; 0.155 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 51 ; 0.144 ; 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): 2679 ; 0.535 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4208 ; 0.861 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1581 ; 1.491 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1373 ; 2.206 ; 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 : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3FSJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000050988. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : ADJUSTABLE FOCUSING MIRRORS IN K REMARK 200 -B GEOMETRY REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 111618 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.370 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.900 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 1BFD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL PH 8.5, 150 MM CACL2, REMARK 280 0.5% V/V MPD [2-METHYL-2,4-PENTANEDIOL], 22% V/V PEG 400, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.74200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.67700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.56950 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.74200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.67700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.56950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.74200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.67700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.56950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.74200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.67700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.56950 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -132.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 81.48400 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 81.48400 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 X 533 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 662 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 709 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 783 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 981 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 MET X 1 REMARK 465 VAL X 527 REMARK 465 LYS X 528 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO X 526 CA C O CB CG CD 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 X 71 -146.46 48.22 REMARK 500 HIS X 281 -77.28 -138.15 REMARK 500 ASP X 284 65.54 -153.48 REMARK 500 PRO X 447 44.23 -80.55 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 CA X 600 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP X 428 OD1 REMARK 620 2 ASN X 455 OD1 88.6 REMARK 620 3 THR X 457 O 109.0 84.7 REMARK 620 4 D7K X 601 O1A 86.3 173.4 93.1 REMARK 620 5 D7K X 601 O2B 164.8 99.3 84.8 86.7 REMARK 620 6 HOH X 603 O 81.1 86.4 166.3 96.9 86.3 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 D7K X 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA X 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D7K RELATED DB: PDB REMARK 900 BENZALDEHYDE LYASE WITH THE SAME INHIBITOR FORMS THE SAME THDP REMARK 900 ADDUCT REMARK 900 RELATED ID: 3F6B RELATED DB: PDB REMARK 900 BFDC WITH A PYRIDYL INHIBITOR FORMS A DIFFERENT THDP ADDUCT DBREF 3FSJ X 1 528 UNP P20906 MDLC_PSEPU 1 528 SEQRES 1 X 528 MET ALA SER VAL HIS GLY THR THR TYR GLU LEU LEU ARG SEQRES 2 X 528 ARG GLN GLY ILE ASP THR VAL PHE GLY ASN PRO GLY SER SEQRES 3 X 528 ASN GLU LEU PRO PHE LEU LYS ASP PHE PRO GLU ASP PHE SEQRES 4 X 528 ARG TYR ILE LEU ALA LEU GLN GLU ALA CYS VAL VAL GLY SEQRES 5 X 528 ILE ALA ASP GLY TYR ALA GLN ALA SER ARG LYS PRO ALA SEQRES 6 X 528 PHE ILE ASN LEU HIS SER ALA ALA GLY THR GLY ASN ALA SEQRES 7 X 528 MET GLY ALA LEU SER ASN ALA TRP ASN SER HIS SER PRO SEQRES 8 X 528 LEU ILE VAL THR ALA GLY GLN GLN THR ARG ALA MET ILE SEQRES 9 X 528 GLY VAL GLU ALA LEU LEU THR ASN VAL ASP ALA ALA ASN SEQRES 10 X 528 LEU PRO ARG PRO LEU VAL LYS TRP SER TYR GLU PRO ALA SEQRES 11 X 528 SER ALA ALA GLU VAL PRO HIS ALA MET SER ARG ALA ILE SEQRES 12 X 528 HIS MET ALA SER MET ALA PRO GLN GLY PRO VAL TYR LEU SEQRES 13 X 528 SER VAL PRO TYR ASP ASP TRP ASP LYS ASP ALA ASP PRO SEQRES 14 X 528 GLN SER HIS HIS LEU PHE ASP ARG HIS VAL SER SER SER SEQRES 15 X 528 VAL ARG LEU ASN ASP GLN ASP LEU ASP ILE LEU VAL LYS SEQRES 16 X 528 ALA LEU ASN SER ALA SER ASN PRO ALA ILE VAL LEU GLY SEQRES 17 X 528 PRO ASP VAL ASP ALA ALA ASN ALA ASN ALA ASP CYS VAL SEQRES 18 X 528 MET LEU ALA GLU ARG LEU LYS ALA PRO VAL TRP VAL ALA SEQRES 19 X 528 PRO SER ALA PRO ARG CYS PRO PHE PRO THR ARG HIS PRO SEQRES 20 X 528 CYS PHE ARG GLY LEU MET PRO ALA GLY ILE ALA ALA ILE SEQRES 21 X 528 SER GLN LEU LEU GLU GLY HIS ASP VAL VAL LEU VAL ILE SEQRES 22 X 528 GLY ALA PRO VAL PHE ARG TYR HIS GLN TYR ASP PRO GLY SEQRES 23 X 528 GLN TYR LEU LYS PRO GLY THR ARG LEU ILE SER VAL THR SEQRES 24 X 528 CYS ASP PRO LEU GLU ALA ALA ARG ALA PRO MET GLY ASP SEQRES 25 X 528 ALA ILE VAL ALA ASP ILE GLY ALA MET ALA SER ALA LEU SEQRES 26 X 528 ALA ASN LEU VAL GLU GLU SER SER ARG GLN LEU PRO THR SEQRES 27 X 528 ALA ALA PRO GLU PRO ALA LYS VAL ASP GLN ASP ALA GLY SEQRES 28 X 528 ARG LEU HIS PRO GLU THR VAL PHE ASP THR LEU ASN ASP SEQRES 29 X 528 MET ALA PRO GLU ASN ALA ILE TYR LEU ASN GLU SER THR SEQRES 30 X 528 SER THR THR ALA GLN MET TRP GLN ARG LEU ASN MET ARG SEQRES 31 X 528 ASN PRO GLY SER TYR TYR PHE CYS ALA ALA GLY GLY LEU SEQRES 32 X 528 GLY PHE ALA LEU PRO ALA ALA ILE GLY VAL GLN LEU ALA SEQRES 33 X 528 GLU PRO GLU ARG GLN VAL ILE ALA VAL ILE GLY ASP GLY SEQRES 34 X 528 SER ALA ASN TYR SER ILE SER ALA LEU TRP THR ALA ALA SEQRES 35 X 528 GLN TYR ASN ILE PRO THR ILE PHE VAL ILE MET ASN ASN SEQRES 36 X 528 GLY THR TYR GLY ALA LEU ARG TRP PHE ALA GLY VAL LEU SEQRES 37 X 528 GLU ALA GLU ASN VAL PRO GLY LEU ASP VAL PRO GLY ILE SEQRES 38 X 528 ASP PHE ARG ALA LEU ALA LYS GLY TYR GLY VAL GLN ALA SEQRES 39 X 528 LEU LYS ALA ASP ASN LEU GLU GLN LEU LYS GLY SER LEU SEQRES 40 X 528 GLN GLU ALA LEU SER ALA LYS GLY PRO VAL LEU ILE GLU SEQRES 41 X 528 VAL SER THR VAL SER PRO VAL LYS HET D7K X 601 39 HET CA X 600 1 HETNAM D7K 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(S)- HETNAM 2 D7K HYDROXY[(R)-HYDROXY(METHOXY)PHOSPHORYL]PHENYLMETHYL}- HETNAM 3 D7K 5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)- HETNAM 4 D7K 4-METHYL-1,3-THIAZOL-3-IUM HETNAM CA CALCIUM ION FORMUL 2 D7K C20 H28 N4 O11 P3 S 1+ FORMUL 3 CA CA 2+ FORMUL 4 HOH *485(H2 O) HELIX 1 1 SER X 3 GLN X 15 1 13 HELIX 2 2 GLY X 25 ASN X 27 5 3 HELIX 3 3 GLU X 28 LYS X 33 1 6 HELIX 4 4 GLN X 46 ARG X 62 1 17 HELIX 5 5 SER X 71 ALA X 78 1 8 HELIX 6 6 ALA X 78 SER X 88 1 11 HELIX 7 7 THR X 100 GLY X 105 1 6 HELIX 8 8 ASP X 114 LEU X 118 5 5 HELIX 9 9 SER X 131 ALA X 133 5 3 HELIX 10 10 GLU X 134 MET X 148 1 15 HELIX 11 11 ASP X 161 TRP X 163 5 3 HELIX 12 12 ASP X 168 PHE X 175 5 8 HELIX 13 13 ASN X 186 ALA X 200 1 15 HELIX 14 14 GLY X 208 ALA X 214 1 7 HELIX 15 15 ALA X 216 LYS X 228 1 13 HELIX 16 16 GLY X 256 GLU X 265 1 10 HELIX 17 17 ASP X 301 ALA X 308 1 8 HELIX 18 18 ASP X 317 VAL X 329 1 13 HELIX 19 19 HIS X 354 ALA X 366 1 13 HELIX 20 20 THR X 379 LEU X 387 1 9 HELIX 21 21 PHE X 405 GLU X 417 1 13 HELIX 22 22 GLY X 429 TYR X 433 5 5 HELIX 23 23 SER X 434 SER X 436 5 3 HELIX 24 24 ALA X 437 ASN X 445 1 9 HELIX 25 25 TYR X 458 GLU X 469 1 12 HELIX 26 26 ASP X 482 GLY X 491 1 10 HELIX 27 27 ASN X 499 ALA X 513 1 15 SHEET 1 A 6 ARG X 40 LEU X 43 0 SHEET 2 A 6 THR X 19 GLY X 22 1 N VAL X 20 O ILE X 42 SHEET 3 A 6 ALA X 65 HIS X 70 1 O PHE X 66 N PHE X 21 SHEET 4 A 6 LEU X 92 GLN X 98 1 O ILE X 93 N ILE X 67 SHEET 5 A 6 VAL X 154 PRO X 159 1 O LEU X 156 N VAL X 94 SHEET 6 A 6 SER X 126 TYR X 127 1 N TYR X 127 O SER X 157 SHEET 1 B 6 PHE X 249 LEU X 252 0 SHEET 2 B 6 VAL X 231 VAL X 233 1 N VAL X 231 O ARG X 250 SHEET 3 B 6 ALA X 204 LEU X 207 1 N ILE X 205 O TRP X 232 SHEET 4 B 6 VAL X 269 ILE X 273 1 O ILE X 273 N VAL X 206 SHEET 5 B 6 ARG X 294 THR X 299 1 O VAL X 298 N VAL X 272 SHEET 6 B 6 ASP X 312 VAL X 315 1 O ASP X 312 N SER X 297 SHEET 1 C 6 TYR X 395 PHE X 397 0 SHEET 2 C 6 ILE X 371 GLU X 375 1 N ASN X 374 O TYR X 396 SHEET 3 C 6 VAL X 422 GLY X 427 1 O VAL X 425 N LEU X 373 SHEET 4 C 6 ILE X 449 ASN X 454 1 O VAL X 451 N ALA X 424 SHEET 5 C 6 VAL X 517 SER X 522 1 O VAL X 521 N ILE X 452 SHEET 6 C 6 GLN X 493 ALA X 497 1 N ALA X 497 O GLU X 520 LINK OD1 ASP X 428 CA CA X 600 1555 1555 2.32 LINK OD1 ASN X 455 CA CA X 600 1555 1555 2.33 LINK O THR X 457 CA CA X 600 1555 1555 2.28 LINK CA CA X 600 O1A D7K X 601 1555 1555 2.19 LINK CA CA X 600 O2B D7K X 601 1555 1555 2.32 LINK CA CA X 600 O HOH X 603 1555 1555 2.29 CISPEP 1 ARG X 120 PRO X 121 0 5.57 CISPEP 2 ALA X 149 PRO X 150 0 -7.99 CISPEP 3 VAL X 277 PHE X 278 0 -18.73 SITE 1 AC1 28 ASN X 23 PRO X 24 GLY X 25 SER X 26 SITE 2 AC1 28 GLU X 47 HIS X 70 ASN X 77 LEU X 110 SITE 3 AC1 28 HIS X 281 THR X 377 SER X 378 PHE X 397 SITE 4 AC1 28 GLY X 401 LEU X 403 GLY X 427 ASP X 428 SITE 5 AC1 28 GLY X 429 SER X 430 TYR X 433 ASN X 455 SITE 6 AC1 28 THR X 457 TYR X 458 GLY X 459 ALA X 460 SITE 7 AC1 28 LEU X 461 PHE X 464 CA X 600 HOH X 717 SITE 1 AC2 5 ASP X 428 ASN X 455 THR X 457 D7K X 601 SITE 2 AC2 5 HOH X 603 CRYST1 81.484 95.354 137.139 90.00 90.00 90.00 I 2 2 2 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 0.012272 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010487 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007292 0.00000