HEADER LYASE 05-NOV-08 3F6B TITLE CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE IN COMPLEX WITH THE TITLE 2 PYRIDYL INHIBITOR PAA 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 EXPDTA X-RAY DIFFRACTION AUTHOR G.S.BRANDT,M.J.MCLEISH,G.L.KENYON,G.A.PETSKO,D.RINGE,F.JORDAN REVDAT 4 06-SEP-23 3F6B 1 REMARK LINK REVDAT 3 25-OCT-17 3F6B 1 REMARK REVDAT 2 17-MAR-09 3F6B 1 JRNL REVDAT 1 09-DEC-08 3F6B 0 JRNL AUTH S.CHAKRABORTY,N.S.NEMERIA,A.BALAKRISHNAN,G.S.BRANDT, JRNL AUTH 2 M.M.KNEEN,A.YEP,M.J.MCLEISH,G.L.KENYON,G.A.PETSKO,D.RINGE, JRNL AUTH 3 F.JORDAN JRNL TITL DETECTION AND TIME COURSE OF FORMATION OF MAJOR THIAMIN JRNL TITL 2 DIPHOSPHATE-BOUND COVALENT INTERMEDIATES DERIVED FROM A JRNL TITL 3 CHROMOPHORIC SUBSTRATE ANALOGUE ON BENZOYLFORMATE JRNL TITL 4 DECARBOXYLASE. JRNL REF BIOCHEMISTRY V. 48 981 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19140682 JRNL DOI 10.1021/BI801810H REMARK 2 REMARK 2 RESOLUTION. 1.34 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 114737 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5750 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) : 1.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6731 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 359 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3941 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 462 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.11000 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): 0.050 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.051 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.030 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.725 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4100 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5610 ; 1.863 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 526 ; 6.090 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;34.102 ;24.451 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 612 ;11.879 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;12.954 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 630 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3178 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1850 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2852 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 308 ; 0.144 ; 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): 128 ; 0.164 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 62 ; 0.358 ; 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): 2693 ; 1.133 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4233 ; 1.581 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1597 ; 2.716 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1376 ; 3.874 ; 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 3F6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050200. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 120069 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9110 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1BFD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 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 40.77000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.03500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.67700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.77000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.03500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.67700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.77000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.03500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.67700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.77000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.03500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.67700 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: 25050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -132.6 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 163.08000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 96.07000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 163.08000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 274.70800 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 96.07000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 274.70800 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 714 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 730 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 802 LIES ON A SPECIAL POSITION. 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 -147.15 44.86 REMARK 500 ASN X 202 63.68 -152.30 REMARK 500 HIS X 281 -66.22 -133.89 REMARK 500 ASP X 284 65.00 -158.15 REMARK 500 PRO X 337 150.08 -49.70 REMARK 500 GLU X 375 48.03 -145.05 REMARK 500 CYS X 398 112.22 -37.80 REMARK 500 PRO X 447 47.41 -85.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 1. 8PA IS A COVALENT ADDUCT BETWEEN 3-(PYRIDIN-3-YL) REMARK 600 ACRYLALDEHYDE AND THE THDP COFACTOR. REMARK 600 2. ACCORDING TO AUTHORS, BOTH RELATED ENTRIES 3F6B REMARK 600 AND 3F6E HAVE THE SAME SUBSTRATE-COFACTOR ADDUCT. THESE REMARK 600 STRUCTURES WERE SOLVED IN SUPPORT OF ENZYMOLOGICAL REMARK 600 EXPERIMENTS WITH BENZOYLFORMATE DECARBOXYLASE. THE ENZYME REMARK 600 DECARBOXYLATES THE 3-PKB SUBSTRATE TO GENERATE AN ALDEHYDE. REMARK 600 THIS ALDEHYDE IS PAA, THE SUBSTRATE APPLIED IN THE REMARK 600 EXPERIMENTS THAT GAVE RISE TO 3F6B STRUCTURE. WHEN AUTHORS REMARK 600 CRYSTALLIZE THE ENZYME IN THE PRESENCE OF 3-PKB, THE SPECIES REMARK 600 THAT IS GENERATED THAN TRAPPED IS PAA, VIA REACTION WITH THE REMARK 600 THIAZOLIUM YLID OF THE THDP COFACTOR TO GENERATE THE ADDUCT REMARK 600 SEEN IN BOTH STRUCTURES. THE 3-PKB INHIBITOR WAS DESIGNED REMARK 600 FIRST, AND THEN PAA WAS DEVELOPED TO CHECK THE HYPOTHESIS REMARK 600 THAT 3-PKB IS CONVERTED TO PAA IN THE ACTIVE SITE. INDEED, REMARK 600 THE ADDUCT IS THE SAME IN 3F6B AND 3F6E. 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 X 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH X 527 O REMARK 620 2 8PA X 602 O1B 87.1 REMARK 620 3 8PA X 602 O2A 96.0 83.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 8PA X 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F6E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE IN COMPLEX WITH REMARK 900 THE PYRIDYL INHIBITOR 3-PKB DBREF 3F6B X 2 526 UNP P20906 MDLC_PSEPU 2 526 SEQRES 1 X 525 ALA SER VAL HIS GLY THR THR TYR GLU LEU LEU ARG ARG SEQRES 2 X 525 GLN GLY ILE ASP THR VAL PHE GLY ASN PRO GLY SER ASN SEQRES 3 X 525 GLU LEU PRO PHE LEU LYS ASP PHE PRO GLU ASP PHE ARG SEQRES 4 X 525 TYR ILE LEU ALA LEU GLN GLU ALA CYS VAL VAL GLY ILE SEQRES 5 X 525 ALA ASP GLY TYR ALA GLN ALA SER ARG LYS PRO ALA PHE SEQRES 6 X 525 ILE ASN LEU HIS SER ALA ALA GLY THR GLY ASN ALA MET SEQRES 7 X 525 GLY ALA LEU SER ASN ALA TRP ASN SER HIS SER PRO LEU SEQRES 8 X 525 ILE VAL THR ALA GLY GLN GLN THR ARG ALA MET ILE GLY SEQRES 9 X 525 VAL GLU ALA LEU LEU THR ASN VAL ASP ALA ALA ASN LEU SEQRES 10 X 525 PRO ARG PRO LEU VAL LYS TRP SER TYR GLU PRO ALA SER SEQRES 11 X 525 ALA ALA GLU VAL PRO HIS ALA MET SER ARG ALA ILE HIS SEQRES 12 X 525 MET ALA SER MET ALA PRO GLN GLY PRO VAL TYR LEU SER SEQRES 13 X 525 VAL PRO TYR ASP ASP TRP ASP LYS ASP ALA ASP PRO GLN SEQRES 14 X 525 SER HIS HIS LEU PHE ASP ARG HIS VAL SER SER SER VAL SEQRES 15 X 525 ARG LEU ASN ASP GLN ASP LEU ASP ILE LEU VAL LYS ALA SEQRES 16 X 525 LEU ASN SER ALA SER ASN PRO ALA ILE VAL LEU GLY PRO SEQRES 17 X 525 ASP VAL ASP ALA ALA ASN ALA ASN ALA ASP CYS VAL MET SEQRES 18 X 525 LEU ALA GLU ARG LEU LYS ALA PRO VAL TRP VAL ALA PRO SEQRES 19 X 525 SER ALA PRO ARG CYS PRO PHE PRO THR ARG HIS PRO CYS SEQRES 20 X 525 PHE ARG GLY LEU MET PRO ALA GLY ILE ALA ALA ILE SER SEQRES 21 X 525 GLN LEU LEU GLU GLY HIS ASP VAL VAL LEU VAL ILE GLY SEQRES 22 X 525 ALA PRO VAL PHE ARG TYR HIS GLN TYR ASP PRO GLY GLN SEQRES 23 X 525 TYR LEU LYS PRO GLY THR ARG LEU ILE SER VAL THR CYS SEQRES 24 X 525 ASP PRO LEU GLU ALA ALA ARG ALA PRO MET GLY ASP ALA SEQRES 25 X 525 ILE VAL ALA ASP ILE GLY ALA MET ALA SER ALA LEU ALA SEQRES 26 X 525 ASN LEU VAL GLU GLU SER SER ARG GLN LEU PRO THR ALA SEQRES 27 X 525 ALA PRO GLU PRO ALA LYS VAL ASP GLN ASP ALA GLY ARG SEQRES 28 X 525 LEU HIS PRO GLU THR VAL PHE ASP THR LEU ASN ASP MET SEQRES 29 X 525 ALA PRO GLU ASN ALA ILE TYR LEU ASN GLU SER THR SER SEQRES 30 X 525 THR THR ALA GLN MET TRP GLN ARG LEU ASN MET ARG ASN SEQRES 31 X 525 PRO GLY SER TYR TYR PHE CYS ALA ALA GLY GLY LEU GLY SEQRES 32 X 525 PHE ALA LEU PRO ALA ALA ILE GLY VAL GLN LEU ALA GLU SEQRES 33 X 525 PRO GLU ARG GLN VAL ILE ALA VAL ILE GLY ASP GLY SER SEQRES 34 X 525 ALA ASN TYR SER ILE SER ALA LEU TRP THR ALA ALA GLN SEQRES 35 X 525 TYR ASN ILE PRO THR ILE PHE VAL ILE MET ASN ASN GLY SEQRES 36 X 525 THR TYR GLY ALA LEU ARG TRP PHE ALA GLY VAL LEU GLU SEQRES 37 X 525 ALA GLU ASN VAL PRO GLY LEU ASP VAL PRO GLY ILE ASP SEQRES 38 X 525 PHE ARG ALA LEU ALA LYS GLY TYR GLY VAL GLN ALA LEU SEQRES 39 X 525 LYS ALA ASP ASN LEU GLU GLN LEU LYS GLY SER LEU GLN SEQRES 40 X 525 GLU ALA LEU SER ALA LYS GLY PRO VAL LEU ILE GLU VAL SEQRES 41 X 525 SER THR VAL SER PRO HET MG X 601 1 HET 8PA X 602 36 HETNAM MG MAGNESIUM ION HETNAM 8PA 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)- HETNAM 2 8PA HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-[(1S,2E)- HETNAM 3 8PA 1-HYDROXY-3-PYRIDIN-3-YLPROP-2-EN-1-YL]-4-METHYL-1,3- HETNAM 4 8PA THIAZOL-3-IUM FORMUL 2 MG MG 2+ FORMUL 3 8PA C20 H26 N5 O8 P2 S 1+ FORMUL 4 HOH *462(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 THR X 95 N LEU X 69 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 LEU X 207 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 ILE X 296 N VAL X 272 SHEET 6 B 6 ASP X 312 VAL X 315 1 O ILE X 314 N THR X 299 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 O HOH X 527 MG MG X 601 1555 1555 2.40 LINK MG MG X 601 O1B 8PA X 602 1555 1555 2.36 LINK MG MG X 601 O2A 8PA X 602 1555 1555 2.24 CISPEP 1 ARG X 120 PRO X 121 0 7.18 CISPEP 2 ALA X 149 PRO X 150 0 -7.90 CISPEP 3 VAL X 277 PHE X 278 0 -23.72 SITE 1 AC1 5 ASP X 428 ASN X 455 THR X 457 HOH X 527 SITE 2 AC1 5 8PA X 602 SITE 1 AC2 26 ASN X 23 PRO X 24 GLY X 25 SER X 26 SITE 2 AC2 26 GLU X 47 HIS X 70 ASN X 77 HIS X 281 SITE 3 AC2 26 GLU X 375 THR X 377 SER X 378 GLY X 401 SITE 4 AC2 26 LEU X 403 GLY X 427 ASP X 428 GLY X 429 SITE 5 AC2 26 SER X 430 TYR X 433 ASN X 455 THR X 457 SITE 6 AC2 26 TYR X 458 GLY X 459 ALA X 460 MG X 601 SITE 7 AC2 26 HOH X 621 HOH X 689 CRYST1 81.540 96.070 137.354 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 0.012264 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010409 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007280 0.00000