PDB Short entry for 1BFD HEADER LYASE 30-APR-98 1BFD TITLE BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: BENZOYLFORMATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.1.1.7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 STRAIN: RF4738; SOURCE 5 ATCC: ATCC 12633; SOURCE 6 COLLECTION: ATCC 12633; SOURCE 7 GENE: MDLC; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: JM105; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PKK233-2; SOURCE 12 EXPRESSION_SYSTEM_GENE: MDLC KEYWDS LYASE, CARBON-CARBON, DECARBOXYLASE, MANDELATE CATABOLISM, THIAMIN KEYWDS 2 DIPHOSPHATE EXPDTA X-RAY DIFFRACTION AUTHOR M.S.HASSON,A.MUSCATE,M.J.MCLEISH,L.S.POLOVNIKOVA,J.A.GERLT, AUTHOR 2 G.L.KENYON,G.A.PETSKO,D.RINGE REVDAT 5 07-FEB-24 1BFD 1 REMARK LINK REVDAT 4 16-NOV-11 1BFD 1 HETATM REVDAT 3 13-JUL-11 1BFD 1 VERSN REVDAT 2 24-FEB-09 1BFD 1 VERSN REVDAT 1 24-JUN-98 1BFD 0 JRNL AUTH M.S.HASSON,A.MUSCATE,M.J.MCLEISH,L.S.POLOVNIKOVA,J.A.GERLT, JRNL AUTH 2 G.L.KENYON,G.A.PETSKO,D.RINGE JRNL TITL THE CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE AT 1.6 JRNL TITL 2 A RESOLUTION: DIVERSITY OF CATALYTIC RESIDUES IN THIAMIN JRNL TITL 3 DIPHOSPHATE-DEPENDENT ENZYMES. JRNL REF BIOCHEMISTRY V. 37 9918 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9665697 JRNL DOI 10.1021/BI973047E REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.S.HASSON,A.MUSCATE,G.T.HENEHAN,P.F.GUIDINGER,G.A.PETSKO, REMARK 1 AUTH 2 D.RINGE,G.L.KENYON REMARK 1 TITL PURIFICATION AND CRYSTALLIZATION OF BENZOYLFORMATE REMARK 1 TITL 2 DECARBOXYLASE REMARK 1 REF PROTEIN SCI. V. 4 955 1995 REMARK 1 REFN ISSN 0961-8368 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.6 REMARK 3 NUMBER OF REFLECTIONS : 56642 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 SET) : 0.152 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2817 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 31.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3497 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 179 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 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 : 29 REMARK 3 SOLVENT ATOMS : 346 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50 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) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.440 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.040 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.530 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.310 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.620 ; 2.500 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: REMARK 3 VAL 524 IS THE LAST RESIDUE FOR WHICH INTERPRETABLE REMARK 3 ELECTRON DENSITY WAS PRESENT. REMARK 4 REMARK 4 1BFD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171689. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAR-94 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 7.0-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS, MOSFLM REMARK 200 DATA SCALING SOFTWARE : RIGAKU REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59179 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 32.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: PROTSYS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN AT ROOM REMARK 280 TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL REMARK 280 SOLUTION OF 22% (V/V) POLYETHYLENE GLYCOL WITH AN AVERAGE REMARK 280 MOLECULAR WEIGHT OF 400 KDA (PEG 400), 0.15 M CACL2, 0.5% (V/V) REMARK 280 MPD, 0.1 M TRISCL (PH 8.5). DROPS CONTAINED EQUAL VOLUMES (2 REMARK 280 MICROL) OF WELL SOLUTION AND PURIFIED BENZOYLFORMATE REMARK 280 DECARBOXYLASE [10 MG/ML IN 0.1 MM MGCL2, 0.2 MM TDP, 25 MM REMARK 280 NAHEPES (PH 7.0)]., VAPOR DIFFUSION - HANGING DROP, VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 41.15000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.30000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 69.15000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.15000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.30000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.15000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.15000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.30000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.15000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.15000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.30000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 69.15000 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: 26700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -231.0 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 164.60000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 96.60000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 164.60000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 276.60000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 96.60000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 276.60000 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 792 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 798 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 803 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: 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 -145.43 42.74 REMARK 500 HIS A 281 -73.97 -134.55 REMARK 500 GLU A 375 43.79 -142.69 REMARK 500 CYS A 398 109.86 -48.39 REMARK 500 PRO A 447 44.75 -66.99 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 532 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 37 O REMARK 620 2 ASP A 364 OD1 77.6 REMARK 620 3 HOH A 691 O 143.2 67.6 REMARK 620 4 HOH A 700 O 70.5 144.2 136.6 REMARK 620 5 HOH A 703 O 95.0 97.8 78.9 69.8 REMARK 620 6 HOH A 844 O 91.9 80.1 93.4 116.1 172.2 REMARK 620 7 HOH A 845 O 138.6 143.1 75.6 68.5 76.1 101.0 REMARK 620 N 1 2 3 4 5 6 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 118.6 REMARK 620 3 LEU A 118 O 74.2 164.6 REMARK 620 4 LEU A 118 O 164.6 74.2 94.7 REMARK 620 5 ARG A 120 O 93.4 81.7 89.4 97.2 REMARK 620 6 ARG A 120 O 81.7 93.4 97.2 89.4 170.3 REMARK 620 7 HOH A 803 O 59.3 59.3 132.6 132.6 85.2 85.2 REMARK 620 8 HOH A 803 O 59.3 59.3 132.6 132.6 85.2 85.2 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 529 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 428 OD1 REMARK 620 2 ASN A 455 OD1 84.2 REMARK 620 3 THR A 457 O 110.3 81.7 REMARK 620 4 TPP A 530 O2A 86.7 170.4 98.6 REMARK 620 5 TPP A 530 O1B 164.0 101.4 85.4 88.2 REMARK 620 6 HOH A 533 O 77.7 84.9 163.5 96.2 87.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CA1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: DIVALENT CATION BOUND TO PYROPHOSPHATE OF TPP REMARK 800 (CA 529). REMARK 800 REMARK 800 SITE_IDENTIFIER: MG1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: MAGNESIUM ION ON CRYSTALLOGRAPHIC TWO-FOLD AT REMARK 800 DIMER INTERFACE (MG 531). REMARK 800 REMARK 800 SITE_IDENTIFIER: CA2 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CALCIUM ION AT CRYSTAL CONTACT (CA 532). REMARK 800 REMARK 800 SITE_IDENTIFIER: PP2 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: POLYPROLINE TYPE II HELIX FROM ARG 334 THROUGH REMARK 800 VAL 346. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 529 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 531 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 532 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TPP A 530 DBREF 1BFD A 1 528 UNP P20906 MDLC_PSEPU 1 528 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 GLU 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 CA A 529 1 HET MG A 531 1 HET CA A 532 1 HET TPP A 530 26 HETNAM CA CALCIUM ION HETNAM MG MAGNESIUM ION HETNAM TPP THIAMINE DIPHOSPHATE FORMUL 2 CA 2(CA 2+) FORMUL 3 MG MG 2+ FORMUL 5 TPP C12 H19 N4 O7 P2 S 1+ FORMUL 6 HOH *346(H2 O) HELIX 1 1 VAL A 4 ARG A 14 1 11 HELIX 2 2 SER A 26 LEU A 32 5 7 HELIX 3 3 GLU A 47 SER A 61 1 15 HELIX 4 4 SER A 71 ASN A 87 1 17 HELIX 5 5 ARG A 101 ILE A 104 1 4 HELIX 6 6 ALA A 115 PRO A 119 1 5 HELIX 7 7 ALA A 132 SER A 147 5 16 HELIX 8 8 TYR A 160 ASP A 162 5 3 HELIX 9 9 PRO A 169 LEU A 174 5 6 HELIX 10 10 ASP A 187 SER A 199 1 13 HELIX 11 11 PRO A 209 ALA A 213 1 5 HELIX 12 12 ASN A 217 LEU A 227 1 11 HELIX 13 13 ILE A 257 LEU A 264 1 8 HELIX 14 14 PRO A 302 ARG A 307 1 6 HELIX 15 15 ILE A 318 LEU A 328 1 11 HELIX 16 16 PRO A 355 MET A 365 1 11 HELIX 17 17 THR A 377 ARG A 386 5 10 HELIX 18 18 ALA A 406 ALA A 416 1 11 HELIX 19 19 ASP A 428 TYR A 444 1 17 HELIX 20 20 GLY A 459 VAL A 467 1 9 HELIX 21 21 PHE A 483 GLY A 489 1 7 HELIX 22 22 LEU A 500 SER A 512 1 13 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 ARG A 40 SHEET 3 A 6 ALA A 65 HIS A 70 1 N PHE A 66 O PHE A 21 SHEET 4 A 6 LEU A 92 GLN A 98 1 N ILE A 93 O ALA A 65 SHEET 5 A 6 VAL A 154 PRO A 159 1 N VAL A 154 O VAL A 94 SHEET 6 A 6 TRP A 125 GLU A 128 1 N TRP A 125 O TYR A 155 SHEET 1 B 6 ASP A 312 VAL A 315 0 SHEET 2 B 6 ARG A 294 THR A 299 1 N SER A 297 O ASP A 312 SHEET 3 B 6 VAL A 269 ILE A 273 1 N VAL A 270 O ARG A 294 SHEET 4 B 6 ALA A 204 LEU A 207 1 N ALA A 204 O LEU A 271 SHEET 5 B 6 PRO A 230 VAL A 233 1 N PRO A 230 O ILE A 205 SHEET 6 B 6 PHE A 249 LEU A 252 1 N ARG A 250 O VAL A 231 SHEET 1 C 6 TYR A 395 PHE A 397 0 SHEET 2 C 6 ILE A 371 GLU A 375 1 N TYR A 372 O TYR A 396 SHEET 3 C 6 VAL A 422 GLY A 427 1 N ILE A 423 O ILE A 371 SHEET 4 C 6 ILE A 449 ASN A 454 1 N ILE A 449 O ALA A 424 SHEET 5 C 6 VAL A 517 SER A 522 1 N VAL A 517 O PHE A 450 SHEET 6 C 6 GLN A 493 ALA A 497 1 N GLN A 493 O LEU A 518 LINK O GLU A 37 CA CA A 532 8557 1555 2.37 LINK O ASN A 117 MG MG A 531 1555 1555 2.50 LINK O ASN A 117 MG MG A 531 2765 1555 2.50 LINK O LEU A 118 MG MG A 531 1555 1555 2.32 LINK O LEU A 118 MG MG A 531 2765 1555 2.32 LINK O ARG A 120 MG MG A 531 1555 1555 2.34 LINK O ARG A 120 MG MG A 531 2765 1555 2.34 LINK OD1 ASP A 364 CA CA A 532 1555 1555 2.52 LINK OD1 ASP A 428 CA CA A 529 1555 1555 2.40 LINK OD1 ASN A 455 CA CA A 529 1555 1555 2.39 LINK O THR A 457 CA CA A 529 1555 1555 2.25 LINK CA CA A 529 O2A TPP A 530 1555 1555 2.26 LINK CA CA A 529 O1B TPP A 530 1555 1555 2.30 LINK CA CA A 529 O HOH A 533 1555 1555 2.39 LINK MG MG A 531 O HOH A 803 1555 1555 2.98 LINK MG MG A 531 O HOH A 803 1555 2765 2.98 LINK CA CA A 532 O HOH A 691 1555 1555 2.48 LINK CA CA A 532 O HOH A 700 1555 8557 2.81 LINK CA CA A 532 O HOH A 703 1555 1555 2.28 LINK CA CA A 532 O HOH A 844 1555 1555 2.30 LINK CA CA A 532 O HOH A 845 1555 1555 2.38 CISPEP 1 ARG A 120 PRO A 121 0 0.20 CISPEP 2 ALA A 149 PRO A 150 0 -0.12 CISPEP 3 VAL A 277 PHE A 278 0 -3.33 SITE 1 CA1 1 CA A 529 SITE 1 MG1 1 MG A 531 SITE 1 CA2 1 CA A 532 SITE 1 PP2 13 ARG A 334 GLN A 335 LEU A 336 PRO A 337 SITE 2 PP2 13 THR A 338 ALA A 339 ALA A 340 PRO A 341 SITE 3 PP2 13 GLU A 342 PRO A 343 ALA A 344 LYS A 345 SITE 4 PP2 13 VAL A 346 SITE 1 AC1 5 ASP A 428 ASN A 455 THR A 457 TPP A 530 SITE 2 AC1 5 HOH A 533 SITE 1 AC2 4 ASN A 117 LEU A 118 ARG A 120 HOH A 803 SITE 1 AC3 7 GLU A 37 ASP A 364 HOH A 691 HOH A 700 SITE 2 AC3 7 HOH A 703 HOH A 844 HOH A 845 SITE 1 AC4 22 ASN A 23 PRO A 24 GLY A 25 GLU A 47 SITE 2 AC4 22 HIS A 70 ASN A 77 THR A 377 SER A 378 SITE 3 AC4 22 GLY A 401 LEU A 403 GLY A 427 ASP A 428 SITE 4 AC4 22 GLY A 429 SER A 430 TYR A 433 ASN A 455 SITE 5 AC4 22 THR A 457 TYR A 458 GLY A 459 ALA A 460 SITE 6 AC4 22 CA A 529 HOH A 540 CRYST1 82.300 96.600 138.300 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 0.012151 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007231 0.00000