HEADER LYASE 24-JAN-05 1YNO TITLE HIGH RESOLUTION STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE FROM TITLE 2 PSEUDOMONAS PUTIDA COMPLEXED WITH THIAMINE THIAZOLONE DIPHOSPHATE CAVEAT 1YNO CHIRALITY ERROR AT THE CB CENTER OF VALINE A 106 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BENZOYLFORMATE DECARBOXYLASE; COMPND 3 CHAIN: A; 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 GENE: MDLC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM105; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PKK233-2 KEYWDS LYASE, CARBON-CARBON, DECARBOXYLASE, MANDELATE CATABOLISM, THIAMINE KEYWDS 2 THIAZOLONE DIPHOSPHATE, HIGH RESOLUTION EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,M.S.HASSON REVDAT 4 23-AUG-23 1YNO 1 REMARK LINK REVDAT 3 13-JUL-11 1YNO 1 VERSN REVDAT 2 24-FEB-09 1YNO 1 VERSN REVDAT 1 17-JAN-06 1YNO 0 JRNL AUTH A.K.BERA,N.L.ANDERSON,M.S.HASSON JRNL TITL HIGH RESOLUTION STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE JRNL TITL 2 FROM PSEUDOMONAS PUTIDA COMPLEXED WITH THIAMINE THIAZOLONE JRNL TITL 3 DIPHOSPHATE; JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.S.HASSON,A.MUSCATE,M.J.MCLEISH,L.S.POLOVNIKOVA,J.A.GERLT, REMARK 1 AUTH 2 G.L.KENYON,G.A.PETSKO,D.RINGE REMARK 1 TITL THE CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE AT 1.6 REMARK 1 TITL 2 ANGSTROM RESOLUTION: DIVERSITY OF CATALYTIC RESIDUES IN REMARK 1 TITL 3 THIAMIN DIPHOSPHATE-DEPENDENT ENZYMES REMARK 1 REF BIOCHEMISTRY V. 37 9918 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 9665697 REMARK 1 DOI 10.1021/BI973047E REMARK 1 REFERENCE 2 REMARK 1 AUTH E.S.POLOVNIKOVA,M.J.MCLEISH,E.A.SERGIENKO,J.T.BURGNER, REMARK 1 AUTH 2 N.L.ANDERSON,A.K.BERA,F.JORDAN,G.L.KENYON,M.S.HASSON REMARK 1 TITL STRUCTURAL AND KINETIC ANALYSIS OF CATALYSIS BY A THIAMIN REMARK 1 TITL 2 DIPHOSPHATE-DEPENDENT ENZYME, BENZOYLFORMATE DECARBOXYLASE. REMARK 1 REF BIOCHEMISTRY V. 42 1820 2003 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 12590569 REMARK 1 DOI 10.1021/BI026490K REMARK 2 REMARK 2 RESOLUTION. 1.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 154627 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 15454 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3934 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 559 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY ? 5% REMARK 4 REMARK 4 1YNO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031724. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-03 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 : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 154631 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.720 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1BFD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400,0.15 M CACL2, 0.5% (V/V) MPD, REMARK 280 0.1 M TRISCL (PH 8.5) , VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 40.47550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.73000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.35050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.47550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.73000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.35050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.47550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.73000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.35050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.47550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.73000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.35050 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 27060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -230.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 95.46000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 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 95.46000 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 MG MG A 531 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 943 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1001 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 PRO A 526 REMARK 465 VAL A 527 REMARK 465 LYS A 528 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 ARG A 13 CA - CB - CG ANGL. DEV. = 15.0 DEGREES REMARK 500 ARG A 40 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -7.2 DEGREES REMARK 500 MET A 103 CG - SD - CE ANGL. DEV. = 14.5 DEGREES REMARK 500 VAL A 106 CA - CB - CG1 ANGL. DEV. = 12.1 DEGREES REMARK 500 VAL A 106 CA - CB - CG1 ANGL. DEV. = -13.6 DEGREES REMARK 500 VAL A 106 CA - CB - CG2 ANGL. DEV. = -13.6 DEGREES REMARK 500 ARG A 120 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 120 NE - CZ - NH2 ANGL. DEV. = 4.6 DEGREES REMARK 500 TYR A 160 CG - CD1 - CE1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 184 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 245 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 HIS A 246 CG - ND1 - CE1 ANGL. DEV. = 6.8 DEGREES REMARK 500 LEU A 263 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 TYR A 283 CB - CG - CD2 ANGL. DEV. = 4.5 DEGREES REMARK 500 TYR A 283 CB - CG - CD2 ANGL. DEV. = 18.6 DEGREES REMARK 500 TYR A 283 CD1 - CG - CD2 ANGL. DEV. = -8.6 DEGREES REMARK 500 TYR A 283 CB - CG - CD1 ANGL. DEV. = -9.9 DEGREES REMARK 500 TYR A 283 CG - CD1 - CE1 ANGL. DEV. = 12.5 DEGREES REMARK 500 ARG A 294 CD - NE - CZ ANGL. DEV. = 13.4 DEGREES REMARK 500 ARG A 294 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 334 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 420 NE - CZ - NH1 ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 420 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 TYR A 458 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 462 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 484 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 GLU A 501 CA - CB - CG ANGL. DEV. = 14.9 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 SER A 71 -146.46 44.67 REMARK 500 LEU A 110 6.11 81.90 REMARK 500 ASN A 202 63.68 -151.59 REMARK 500 HIS A 281 -74.89 -139.69 REMARK 500 PRO A 447 48.57 -85.61 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 A 533 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 37 O REMARK 620 2 ASP A 364 OD1 75.1 REMARK 620 3 HOH A 683 O 72.6 144.6 REMARK 620 4 HOH A 886 O 88.1 79.8 85.2 REMARK 620 5 HOH A1059 O 72.0 129.3 51.0 135.2 REMARK 620 6 HOH A1090 O 143.3 68.3 142.2 85.2 133.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 531 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 117 O REMARK 620 2 ASN A 117 O 114.6 REMARK 620 3 LEU A 118 O 75.2 168.1 REMARK 620 4 LEU A 118 O 168.1 75.2 96.0 REMARK 620 5 ARG A 120 O 93.3 79.7 93.3 95.2 REMARK 620 6 ARG A 120 O 79.7 93.3 95.2 93.3 167.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 534 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 347 OD2 REMARK 620 2 ASP A 347 OD1 51.9 REMARK 620 3 ALA A 416 O 148.6 156.8 REMARK 620 4 HOH A 623 O 106.1 77.5 97.7 REMARK 620 5 HOH A 724 O 81.0 76.4 94.3 139.2 REMARK 620 6 HOH A 816 O 129.6 81.4 75.4 76.7 68.9 REMARK 620 7 HOH A 841 O 84.4 115.4 83.7 72.0 148.3 139.4 REMARK 620 8 HOH A 861 O 76.4 123.4 72.5 146.6 74.1 128.1 75.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 532 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 428 OD1 REMARK 620 2 ASN A 455 OD1 86.8 REMARK 620 3 THR A 457 O 106.3 84.8 REMARK 620 4 TZD A 530 O12 88.5 174.3 93.4 REMARK 620 5 TZD A 530 O21 164.8 102.1 86.9 83.2 REMARK 620 6 HOH A1002 O 81.8 85.4 166.8 97.2 86.6 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 MG A 531 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 532 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 533 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 534 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TZD A 530 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BFD RELATED DB: PDB DBREF 1YNO A 2 528 UNP P20906 MDLC_PSEPU 2 528 SEQRES 1 A 527 ALA SER VAL HIS GLY THR THR TYR GLU LEU LEU ARG ARG SEQRES 2 A 527 GLN GLY ILE ASP THR VAL PHE GLY ASN PRO GLY SER ASN SEQRES 3 A 527 GLU LEU PRO PHE LEU LYS ASP PHE PRO GLU ASP PHE ARG SEQRES 4 A 527 TYR ILE LEU ALA LEU GLN GLU ALA CYS VAL VAL GLY ILE SEQRES 5 A 527 ALA ASP GLY TYR ALA GLN ALA SER ARG LYS PRO ALA PHE SEQRES 6 A 527 ILE ASN LEU HIS SER ALA ALA GLY THR GLY ASN ALA MET SEQRES 7 A 527 GLY ALA LEU SER ASN ALA TRP ASN SER HIS SER PRO LEU SEQRES 8 A 527 ILE VAL THR ALA GLY GLN GLN THR ARG ALA MET ILE GLY SEQRES 9 A 527 VAL GLU ALA LEU LEU THR ASN VAL ASP ALA ALA ASN LEU SEQRES 10 A 527 PRO ARG PRO LEU VAL LYS TRP SER TYR GLU PRO ALA SER SEQRES 11 A 527 ALA ALA GLU VAL PRO HIS ALA MET SER ARG ALA ILE HIS SEQRES 12 A 527 MET ALA SER MET ALA PRO GLN GLY PRO VAL TYR LEU SER SEQRES 13 A 527 VAL PRO TYR ASP ASP TRP ASP LYS ASP ALA ASP PRO GLN SEQRES 14 A 527 SER HIS HIS LEU PHE ASP ARG HIS VAL SER SER SER VAL SEQRES 15 A 527 ARG LEU ASN ASP GLN ASP LEU ASP ILE LEU VAL LYS ALA SEQRES 16 A 527 LEU ASN SER ALA SER ASN PRO ALA ILE VAL LEU GLY PRO SEQRES 17 A 527 ASP VAL ASP ALA ALA ASN ALA ASN ALA ASP CYS VAL MET SEQRES 18 A 527 LEU ALA GLU ARG LEU LYS ALA PRO VAL TRP VAL ALA PRO SEQRES 19 A 527 SER ALA PRO ARG CYS PRO PHE PRO THR ARG HIS PRO CYS SEQRES 20 A 527 PHE ARG GLY LEU MET PRO ALA GLY ILE ALA ALA ILE SER SEQRES 21 A 527 GLN LEU LEU GLU GLY HIS ASP VAL VAL LEU VAL ILE GLY SEQRES 22 A 527 ALA PRO VAL PHE ARG TYR HIS GLN TYR ASP PRO GLY GLN SEQRES 23 A 527 TYR LEU LYS PRO GLY THR ARG LEU ILE SER VAL THR CYS SEQRES 24 A 527 ASP PRO LEU GLU ALA ALA ARG ALA PRO MET GLY ASP ALA SEQRES 25 A 527 ILE VAL ALA ASP ILE GLY ALA MET ALA SER ALA LEU ALA SEQRES 26 A 527 ASN LEU VAL GLU GLU SER SER ARG GLN LEU PRO THR ALA SEQRES 27 A 527 ALA PRO GLU PRO ALA LYS VAL ASP GLN ASP ALA GLY ARG SEQRES 28 A 527 LEU HIS PRO GLU THR VAL PHE ASP THR LEU ASN ASP MET SEQRES 29 A 527 ALA PRO GLU ASN ALA ILE TYR LEU ASN GLU SER THR SER SEQRES 30 A 527 THR THR ALA GLN MET TRP GLN ARG LEU ASN MET ARG ASN SEQRES 31 A 527 PRO GLY SER TYR TYR PHE CYS ALA ALA GLY GLY LEU GLY SEQRES 32 A 527 PHE ALA LEU PRO ALA ALA ILE GLY VAL GLN LEU ALA GLU SEQRES 33 A 527 PRO GLU ARG GLN VAL ILE ALA VAL ILE GLY ASP GLY SER SEQRES 34 A 527 ALA ASN TYR SER ILE SER ALA LEU TRP THR ALA ALA GLN SEQRES 35 A 527 TYR ASN ILE PRO THR ILE PHE VAL ILE MET ASN ASN GLY SEQRES 36 A 527 THR TYR GLY ALA LEU ARG TRP PHE ALA GLY VAL LEU GLU SEQRES 37 A 527 ALA GLU ASN VAL PRO GLY LEU ASP VAL PRO GLY ILE ASP SEQRES 38 A 527 PHE ARG ALA LEU ALA LYS GLY TYR GLY VAL GLN ALA LEU SEQRES 39 A 527 LYS ALA ASP ASN LEU GLU GLN LEU LYS GLY SER LEU GLN SEQRES 40 A 527 GLU ALA LEU SER ALA LYS GLY PRO VAL LEU ILE GLU VAL SEQRES 41 A 527 SER THR VAL SER PRO VAL LYS HET MG A 531 1 HET CA A 532 1 HET CA A 533 1 HET CA A 534 1 HET TZD A 530 27 HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL- HETNAM 2 TZD 2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN HETNAM 3 TZD DIPHOSPHATE HETSYN TZD THIAMIN THIAZOLONE DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 CA 3(CA 2+) FORMUL 6 TZD C12 H18 N4 O8 P2 S FORMUL 7 HOH *559(H2 O) HELIX 1 1 SER A 3 GLN A 15 1 13 HELIX 2 2 GLY A 25 ASN A 27 5 3 HELIX 3 3 GLU A 28 LYS A 33 1 6 HELIX 4 4 GLN A 46 ARG A 62 1 17 HELIX 5 5 SER A 71 ALA A 78 1 8 HELIX 6 6 ALA A 78 SER A 88 1 11 HELIX 7 7 THR A 100 GLY A 105 1 6 HELIX 8 8 ASP A 114 LEU A 118 5 5 HELIX 9 9 SER A 131 ALA A 133 5 3 HELIX 10 10 GLU A 134 MET A 148 1 15 HELIX 11 11 ASP A 161 TRP A 163 5 3 HELIX 12 12 ASP A 168 PHE A 175 5 8 HELIX 13 13 ASN A 186 ALA A 200 1 15 HELIX 14 14 GLY A 208 ASN A 215 1 8 HELIX 15 15 ALA A 216 LYS A 228 1 13 HELIX 16 16 GLY A 256 GLU A 265 1 10 HELIX 17 17 ASP A 301 ALA A 308 1 8 HELIX 18 18 ASP A 317 VAL A 329 1 13 HELIX 19 19 HIS A 354 ALA A 366 1 13 HELIX 20 20 SER A 376 SER A 378 5 3 HELIX 21 21 THR A 379 LEU A 387 1 9 HELIX 22 22 PHE A 405 GLU A 417 1 13 HELIX 23 23 ASP A 428 ASN A 432 1 5 HELIX 24 24 TYR A 433 SER A 436 5 4 HELIX 25 25 ALA A 437 ASN A 445 1 9 HELIX 26 26 TYR A 458 LEU A 468 1 11 HELIX 27 27 ASP A 482 GLY A 491 1 10 HELIX 28 28 ASN A 499 ALA A 513 1 15 SHEET 1 A 6 ARG A 40 LEU A 43 0 SHEET 2 A 6 THR A 19 GLY A 22 1 N VAL A 20 O ILE A 42 SHEET 3 A 6 ALA A 65 HIS A 70 1 O PHE A 66 N PHE A 21 SHEET 4 A 6 LEU A 92 GLN A 98 1 O ILE A 93 N ILE A 67 SHEET 5 A 6 VAL A 154 PRO A 159 1 O LEU A 156 N VAL A 94 SHEET 6 A 6 SER A 126 TYR A 127 1 N TYR A 127 O SER A 157 SHEET 1 B 6 PHE A 249 LEU A 252 0 SHEET 2 B 6 VAL A 231 VAL A 233 1 N VAL A 231 O ARG A 250 SHEET 3 B 6 ALA A 204 LEU A 207 1 N LEU A 207 O TRP A 232 SHEET 4 B 6 VAL A 269 ILE A 273 1 O ILE A 273 N VAL A 206 SHEET 5 B 6 ARG A 294 THR A 299 1 O VAL A 298 N VAL A 272 SHEET 6 B 6 ASP A 312 VAL A 315 1 O ILE A 314 N THR A 299 SHEET 1 C 6 TYR A 395 PHE A 397 0 SHEET 2 C 6 ILE A 371 GLU A 375 1 N ASN A 374 O TYR A 396 SHEET 3 C 6 VAL A 422 GLY A 427 1 O VAL A 425 N GLU A 375 SHEET 4 C 6 ILE A 449 ASN A 454 1 O VAL A 451 N ALA A 424 SHEET 5 C 6 VAL A 517 SER A 522 1 O VAL A 521 N ILE A 452 SHEET 6 C 6 GLN A 493 ALA A 497 1 N LEU A 495 O GLU A 520 LINK O GLU A 37 CA CA A 533 8555 1555 2.32 LINK O ASN A 117 MG MG A 531 1555 1555 2.68 LINK O ASN A 117 MG MG A 531 2565 1555 2.68 LINK O LEU A 118 MG MG A 531 1555 1555 2.46 LINK O LEU A 118 MG MG A 531 2565 1555 2.46 LINK O ARG A 120 MG MG A 531 1555 1555 2.44 LINK O ARG A 120 MG MG A 531 2565 1555 2.44 LINK OD2 ASP A 347 CA CA A 534 8455 1555 2.40 LINK OD1 ASP A 347 CA CA A 534 8455 1555 2.58 LINK OD1 ASP A 364 CA CA A 533 1555 1555 2.39 LINK O ALA A 416 CA CA A 534 1555 1555 2.29 LINK OD1 ASP A 428 CA CA A 532 1555 1555 2.28 LINK OD1 ASN A 455 CA CA A 532 1555 1555 2.26 LINK O THR A 457 CA CA A 532 1555 1555 2.25 LINK O12 TZD A 530 CA CA A 532 1555 1555 2.25 LINK O21 TZD A 530 CA CA A 532 1555 1555 2.28 LINK CA CA A 532 O HOH A1002 1555 1555 2.33 LINK CA CA A 533 O HOH A 683 1555 1555 2.52 LINK CA CA A 533 O HOH A 886 1555 1555 2.57 LINK CA CA A 533 O HOH A1059 1555 1555 2.78 LINK CA CA A 533 O HOH A1090 1555 1555 2.43 LINK CA CA A 534 O HOH A 623 1555 1555 2.41 LINK CA CA A 534 O HOH A 724 1555 8455 2.32 LINK CA CA A 534 O HOH A 816 1555 1555 2.49 LINK CA CA A 534 O HOH A 841 1555 1555 2.45 LINK CA CA A 534 O HOH A 861 1555 1555 2.51 CISPEP 1 ARG A 120 PRO A 121 0 8.00 CISPEP 2 ALA A 149 PRO A 150 0 -8.38 CISPEP 3 VAL A 277 PHE A 278 0 -22.84 SITE 1 AC1 3 ASN A 117 LEU A 118 ARG A 120 SITE 1 AC2 5 ASP A 428 ASN A 455 THR A 457 TZD A 530 SITE 2 AC2 5 HOH A1002 SITE 1 AC3 6 GLU A 37 ASP A 364 HOH A 683 HOH A 886 SITE 2 AC3 6 HOH A1059 HOH A1090 SITE 1 AC4 7 ASP A 347 ALA A 416 HOH A 623 HOH A 724 SITE 2 AC4 7 HOH A 816 HOH A 841 HOH A 861 SITE 1 AC5 23 ASN A 23 PRO A 24 GLY A 25 GLU A 47 SITE 2 AC5 23 HIS A 70 ASN A 77 THR A 377 SER A 378 SITE 3 AC5 23 GLY A 401 LEU A 403 GLY A 427 ASP A 428 SITE 4 AC5 23 GLY A 429 SER A 430 TYR A 433 ASN A 455 SITE 5 AC5 23 THR A 457 TYR A 458 GLY A 459 ALA A 460 SITE 6 AC5 23 CA A 532 HOH A 602 HOH A 919 CRYST1 80.951 95.460 136.701 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 0.012353 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010476 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007315 0.00000