PDB Short entry for 1PI3 HEADER LYASE 29-MAY-03 1PI3 TITLE E28Q MUTANT BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA 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; COMPND 7 MUTATION: 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: RF4738; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PREP7 KEYWDS LYASE, DECARBOXYLASE, MANDELATE CATABOLISM, THIAMIN DIPHOSPHATE, KEYWDS 2 MUTANT, HIGH RESOLUTION EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,M.S.HASSON REVDAT 7 16-AUG-23 1PI3 1 REMARK REVDAT 6 27-OCT-21 1PI3 1 REMARK SEQADV LINK REVDAT 5 11-OCT-17 1PI3 1 REMARK REVDAT 4 13-JUL-11 1PI3 1 VERSN REVDAT 3 24-FEB-09 1PI3 1 VERSN REVDAT 2 26-SEP-06 1PI3 1 HETATM HETNAM REVDAT 1 23-NOV-04 1PI3 0 JRNL AUTH A.K.BERA,M.S.HASSON JRNL TITL HIGH RESOLUTION STRUCTURE OF BENZOYLFORMATE DECARBOXYLATE JRNL TITL 2 E28Q MUTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 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 DOI 10.1021/BI026490K REMARK 1 REFERENCE 2 REMARK 1 AUTH M.S.HASSON,A.MUSCATE,M.J.MCLEISH,E.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 A RESOLUTION: DIVERSITY OF CATALYTIC RESIDUES IN THIAMIN REMARK 1 TITL 3 DIPHOSPHATE-DEPENDENT ENZYMES REMARK 1 REF BIOCHEMISTRY V. 37 9918 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI973047E REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.6 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.121 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.136 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 0.050 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 7287 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 165003 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.107 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 0.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 115356 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3928 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 504 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 4406.9 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 3825.3 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 7 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 40857 REMARK 3 NUMBER OF RESTRAINTS : 49155 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.091 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.084 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.062 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.036 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.079 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) REMARK 4 REMARK 4 1PI3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019332. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 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) : 1.0000 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 : 137252 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: CNS, SHELXL-97 REMARK 200 STARTING MODEL: PDB ENTRY 1BFD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 400, 0.15 M CACL2, 0.5% MPD, REMARK 280 0.1 M TRIS-CL (PH 8.5), 0.1 MM MGCL2, 0.2 MM TZD, 25 MM NA-HEPES REMARK 280 (PH 7.0) VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 8.50 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 40.48000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.76400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.53050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.48000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.76400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.53050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.48000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.76400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.53050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.48000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.76400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.53050 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: 26800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -238.0 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 161.92000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 95.52800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 161.92000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 274.12200 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 95.52800 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 274.12200 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 A 791 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 797 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 802 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 A 1 REMARK 465 SER A 525 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. = 15.7 DEGREES REMARK 500 ARG A 40 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 101 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 MET A 103 CG - SD - CE ANGL. DEV. = -11.5 DEGREES REMARK 500 ARG A 120 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 120 NE - CZ - NH1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 245 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 245 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 HIS A 246 CG - ND1 - CE1 ANGL. DEV. = 10.3 DEGREES REMARK 500 HIS A 246 ND1 - CE1 - NE2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 250 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 294 CD - NE - CZ ANGL. DEV. = 13.4 DEGREES REMARK 500 ARG A 294 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 334 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 352 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 352 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 LEU A 353 CB - CG - CD1 ANGL. DEV. = 11.6 DEGREES REMARK 500 ARG A 390 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 420 NE - CZ - NH1 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 420 NE - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG A 484 NE - CZ - NH2 ANGL. DEV. = -4.6 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 -147.42 48.95 REMARK 500 LEU A 110 5.40 81.67 REMARK 500 ASN A 202 64.95 -151.71 REMARK 500 ALA A 255 53.95 -91.20 REMARK 500 HIS A 281 -72.48 -138.40 REMARK 500 PRO A 447 47.53 -85.15 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 74.6 REMARK 620 3 HOH A 690 O 142.7 68.1 REMARK 620 4 HOH A 699 O 74.3 146.9 141.6 REMARK 620 5 HOH A 728 O 74.7 127.2 130.1 52.8 REMARK 620 N 1 2 3 4 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 120.8 REMARK 620 3 LEU A 118 O 77.4 159.9 REMARK 620 4 LEU A 118 O 170.6 68.6 93.5 REMARK 620 5 ARG A 120 O 97.0 76.9 93.4 85.8 REMARK 620 6 ARG A 120 O 86.5 94.0 95.7 92.1 170.8 REMARK 620 7 HOH A 802 O 61.9 58.9 138.7 127.4 85.4 88.8 REMARK 620 8 HOH A 802 O 61.9 58.9 138.7 127.4 85.4 88.8 0.0 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 534 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 347 OD2 REMARK 620 2 ASP A 347 OD1 51.5 REMARK 620 3 ALA A 416 O 149.4 156.1 REMARK 620 4 HOH A 697 O 77.1 76.8 95.3 REMARK 620 5 HOH A 700 O 128.1 79.7 76.4 75.1 REMARK 620 6 HOH A 711 O 106.8 77.8 97.1 143.0 74.1 REMARK 620 7 HOH A 860 O 83.8 114.5 85.4 143.4 139.4 72.5 REMARK 620 8 HOH A 883 O 75.3 121.8 74.3 69.3 130.9 147.7 75.7 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 87.1 REMARK 620 3 THR A 457 O 105.6 85.4 REMARK 620 4 TZD A 530 O12 89.9 176.5 93.8 REMARK 620 5 TZD A 530 O21 165.7 99.5 87.7 83.9 REMARK 620 6 HOH A 936 O 80.8 85.7 168.8 95.5 86.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 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 REMARK 900 BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA REMARK 900 RELATED ID: 1MCZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AN INHIBITOR, R-MANDELATE DBREF 1PI3 A 1 528 UNP P20906 MDLC_PSEPU 1 528 SEQADV 1PI3 GLN A 28 UNP P20906 GLU 28 ENGINEERED MUTATION SEQRES 1 A 528 MET ALA SER VAL HIS GLY THR THR TYR GLU LEU LEU ARG SEQRES 2 A 528 ARG GLN GLY ILE ASP THR VAL PHE GLY ASN PRO GLY SER SEQRES 3 A 528 ASN GLN LEU PRO PHE LEU LYS ASP PHE PRO GLU ASP PHE SEQRES 4 A 528 ARG TYR ILE LEU ALA LEU GLN GLU ALA CYS VAL VAL GLY SEQRES 5 A 528 ILE ALA ASP GLY TYR ALA GLN ALA SER ARG LYS PRO ALA SEQRES 6 A 528 PHE ILE ASN LEU HIS SER ALA ALA GLY THR GLY ASN ALA SEQRES 7 A 528 MET GLY ALA LEU SER ASN ALA TRP ASN SER HIS SER PRO SEQRES 8 A 528 LEU ILE VAL THR ALA GLY GLN GLN THR ARG ALA MET ILE SEQRES 9 A 528 GLY VAL GLU ALA LEU LEU THR ASN VAL ASP ALA ALA ASN SEQRES 10 A 528 LEU PRO ARG PRO LEU VAL LYS TRP SER TYR GLU PRO ALA SEQRES 11 A 528 SER ALA ALA GLU VAL PRO HIS ALA MET SER ARG ALA ILE SEQRES 12 A 528 HIS MET ALA SER MET ALA PRO GLN GLY PRO VAL TYR LEU SEQRES 13 A 528 SER VAL PRO TYR ASP ASP TRP ASP LYS ASP ALA ASP PRO SEQRES 14 A 528 GLN SER HIS HIS LEU PHE ASP ARG HIS VAL SER SER SER SEQRES 15 A 528 VAL ARG LEU ASN ASP GLN ASP LEU ASP ILE LEU VAL LYS SEQRES 16 A 528 ALA LEU ASN SER ALA SER ASN PRO ALA ILE VAL LEU GLY SEQRES 17 A 528 PRO ASP VAL ASP ALA ALA ASN ALA ASN ALA ASP CYS VAL SEQRES 18 A 528 MET LEU ALA GLU ARG LEU LYS ALA PRO VAL TRP VAL ALA SEQRES 19 A 528 PRO SER ALA PRO ARG CYS PRO PHE PRO THR ARG HIS PRO SEQRES 20 A 528 CYS PHE ARG GLY LEU MET PRO ALA GLY ILE ALA ALA ILE SEQRES 21 A 528 SER GLN LEU LEU GLU GLY HIS ASP VAL VAL LEU VAL ILE SEQRES 22 A 528 GLY ALA PRO VAL PHE ARG TYR HIS GLN TYR ASP PRO GLY SEQRES 23 A 528 GLN TYR LEU LYS PRO GLY THR ARG LEU ILE SER VAL THR SEQRES 24 A 528 CYS ASP PRO LEU GLU ALA ALA ARG ALA PRO MET GLY ASP SEQRES 25 A 528 ALA ILE VAL ALA ASP ILE GLY ALA MET ALA SER ALA LEU SEQRES 26 A 528 ALA ASN LEU VAL GLU GLU SER SER ARG GLN LEU PRO THR SEQRES 27 A 528 ALA ALA PRO GLU PRO ALA LYS VAL ASP GLN ASP ALA GLY SEQRES 28 A 528 ARG LEU HIS PRO GLU THR VAL PHE ASP THR LEU ASN ASP SEQRES 29 A 528 MET ALA PRO GLU ASN ALA ILE TYR LEU ASN GLU SER THR SEQRES 30 A 528 SER THR THR ALA GLN MET TRP GLN ARG LEU ASN MET ARG SEQRES 31 A 528 ASN PRO GLY SER TYR TYR PHE CYS ALA ALA GLY GLY LEU SEQRES 32 A 528 GLY PHE ALA LEU PRO ALA ALA ILE GLY VAL GLN LEU ALA SEQRES 33 A 528 GLU PRO GLU ARG GLN VAL ILE ALA VAL ILE GLY ASP GLY SEQRES 34 A 528 SER ALA ASN TYR SER ILE SER ALA LEU TRP THR ALA ALA SEQRES 35 A 528 GLN TYR ASN ILE PRO THR ILE PHE VAL ILE MET ASN ASN SEQRES 36 A 528 GLY THR TYR GLY ALA LEU ARG TRP PHE ALA GLY VAL LEU SEQRES 37 A 528 GLU ALA GLU ASN VAL PRO GLY LEU ASP VAL PRO GLY ILE SEQRES 38 A 528 ASP PHE ARG ALA LEU ALA LYS GLY TYR GLY VAL GLN ALA SEQRES 39 A 528 LEU LYS ALA ASP ASN LEU GLU GLN LEU LYS GLY SER LEU SEQRES 40 A 528 GLN GLU ALA LEU SER ALA LYS GLY PRO VAL LEU ILE GLU SEQRES 41 A 528 VAL 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 *504(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 GLN 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 ALA A 214 1 7 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 THR A 379 LEU A 387 1 9 HELIX 21 21 PHE A 405 GLU A 417 1 13 HELIX 22 22 GLY A 429 TYR A 433 5 5 HELIX 23 23 SER A 434 SER A 436 5 3 HELIX 24 24 ALA A 437 ASN A 445 1 9 HELIX 25 25 TYR A 458 GLU A 469 1 12 HELIX 26 26 ASP A 482 TYR A 490 1 9 HELIX 27 27 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 LEU A 373 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 8557 1555 2.31 LINK O ASN A 117 MG MG A 531 1555 1555 2.62 LINK O ASN A 117 MG MG A 531 2765 1555 2.94 LINK O LEU A 118 MG MG A 531 1555 1555 2.54 LINK O LEU A 118 MG MG A 531 2765 1555 2.79 LINK O ARG A 120 MG MG A 531 1555 1555 2.70 LINK O ARG A 120 MG MG A 531 2765 1555 2.50 LINK OD2 ASP A 347 CA CA A 534 8457 1555 2.41 LINK OD1 ASP A 347 CA CA A 534 8457 1555 2.60 LINK OD1 ASP A 364 CA CA A 533 1555 1555 2.45 LINK O ALA A 416 CA CA A 534 1555 1555 2.29 LINK OD1 ASP A 428 CA CA A 532 1555 1555 2.26 LINK OD1 ASN A 455 CA CA A 532 1555 1555 2.29 LINK O THR A 457 CA CA A 532 1555 1555 2.24 LINK O12 TZD A 530 CA CA A 532 1555 1555 2.19 LINK O21 TZD A 530 CA CA A 532 1555 1555 2.27 LINK MG MG A 531 O HOH A 802 1555 1555 3.08 LINK MG MG A 531 O HOH A 802 1555 2765 3.08 LINK CA CA A 532 O HOH A 936 1555 1555 2.32 LINK CA CA A 533 O HOH A 690 1555 1555 2.47 LINK CA CA A 533 O HOH A 699 1555 8557 2.58 LINK CA CA A 533 O HOH A 728 1555 8557 2.71 LINK CA CA A 534 O HOH A 697 1555 8457 2.35 LINK CA CA A 534 O HOH A 700 1555 1555 2.50 LINK CA CA A 534 O HOH A 711 1555 1555 2.49 LINK CA CA A 534 O HOH A 860 1555 8457 2.41 LINK CA CA A 534 O HOH A 883 1555 1555 2.42 CISPEP 1 ARG A 120 PRO A 121 0 7.78 CISPEP 2 ALA A 149 PRO A 150 0 -7.63 CISPEP 3 VAL A 277 PHE A 278 0 -23.13 SITE 1 AC1 4 ASN A 117 LEU A 118 ARG A 120 HOH A 802 SITE 1 AC2 5 ASP A 428 ASN A 455 THR A 457 TZD A 530 SITE 2 AC2 5 HOH A 936 SITE 1 AC3 5 GLU A 37 ASP A 364 HOH A 690 HOH A 699 SITE 2 AC3 5 HOH A 728 SITE 1 AC4 7 ASP A 347 ALA A 416 HOH A 697 HOH A 700 SITE 2 AC4 7 HOH A 711 HOH A 860 HOH A 883 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 540 HOH A 626 CRYST1 80.960 95.528 137.061 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 0.012352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010468 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007296 0.00000