HEADER LYASE 23-JAN-10 3LHV
TITLE CRYSTAL STRUCTURE OF THE MUTANT V182A.I199A.V201A OF OROTIDINE 5'-
TITLE 2 MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
TITLE 3 COMPLEXED WITH INHIBITOR BMP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE;
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 SYNONYM: OMP DECARBOXYLASE, OMPDCASE, OMPDECASE;
COMPND 5 EC: 4.1.1.23;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS;
SOURCE 3 ORGANISM_TAXID: 187420;
SOURCE 4 STRAIN: DELTA H;
SOURCE 5 GENE: PYRF, MTH_129;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS MUTANT V182A.I199A.V201A, 6-HYDROXYURIDINE-5'-PHOSPHATE,
KEYWDS 2 DECARBOXYLASE, PYRIMIDINE BIOSYNTHESIS, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.A.FEDOROV,E.V.FEDOROV,B.M.WOOD,J.A.GERLT,S.C.ALMO
REVDAT 3 06-SEP-23 3LHV 1 REMARK
REVDAT 2 13-OCT-21 3LHV 1 REMARK SEQADV
REVDAT 1 16-JUN-10 3LHV 0
JRNL AUTH B.M.WOOD,T.L.AMYES,A.A.FEDOROV,E.V.FEDOROV,A.SHABILA,
JRNL AUTH 2 S.C.ALMO,J.P.RICHARD,J.A.GERLT
JRNL TITL CONFORMATIONAL CHANGES IN OROTIDINE 5'-MONOPHOSPHATE
JRNL TITL 2 DECARBOXYLASE: "REMOTE" RESIDUES THAT STABILIZE THE ACTIVE
JRNL TITL 3 CONFORMATION.
JRNL REF BIOCHEMISTRY V. 49 3514 2010
JRNL REFN ISSN 0006-2960
JRNL PMID 20369850
JRNL DOI 10.1021/BI100443A
REMARK 2
REMARK 2 RESOLUTION. 1.35 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.2
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) : 1.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.90
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1247865.480
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.9
REMARK 3 NUMBER OF REFLECTIONS : 167558
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) : 0.231
REMARK 3 FREE R VALUE : 0.250
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 8414
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) : 1.35
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 58.50
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 17011
REMARK 3 BIN R VALUE (WORKING SET) : 0.3430
REMARK 3 BIN FREE R VALUE : 0.3490
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 835
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6570
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 88
REMARK 3 SOLVENT ATOMS : 580
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 13.90
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.69000
REMARK 3 B22 (A**2) : 1.50000
REMARK 3 B33 (A**2) : 0.19000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -1.88000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19
REMARK 3 ESD FROM SIGMAA (A) : 0.16
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) : 0.21
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.004
REMARK 3 BOND ANGLES (DEGREES) : 1.100
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.80
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890
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) : 0.860 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.380 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.740 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.670 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.45
REMARK 3 BSOL : 51.03
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 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : ION.PARAM
REMARK 3 PARAMETER FILE 4 : BMP_PAR.TXT
REMARK 3 PARAMETER FILE 5 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : ION.TOP
REMARK 3 TOPOLOGY FILE 4 : BMP_TOP.TXT
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
REMARK 4
REMARK 4 3LHV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-10.
REMARK 100 THE DEPOSITION ID IS D_1000057296.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-JUL-09
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 : NSLS
REMARK 200 BEAMLINE : X4A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915
REMARK 200 MONOCHROMATOR : SI 111 CHANNEL
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 : 167558
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350
REMARK 200 RESOLUTION RANGE LOW (A) : 25.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.06600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
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 : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: BALBES
REMARK 200 STARTING MODEL: 3G18
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.68
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M TRIS, 0.2M
REMARK 280 MAGNESIUM CHLORIDE, PH 8.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
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 32.08100
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3410 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 16110 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3410 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 16110 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D
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 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 ARG A 2
REMARK 465 SER A 3
REMARK 465 ARG A 4
REMARK 465 ARG A 5
REMARK 465 VAL A 6
REMARK 465 ASP A 7
REMARK 465 LEU A 226
REMARK 465 ASN A 227
REMARK 465 PRO A 228
REMARK 465 MET B 1
REMARK 465 ARG B 2
REMARK 465 SER B 3
REMARK 465 ARG B 4
REMARK 465 ARG B 5
REMARK 465 VAL B 6
REMARK 465 ASP B 7
REMARK 465 VAL B 8
REMARK 465 LEU B 226
REMARK 465 ASN B 227
REMARK 465 PRO B 228
REMARK 465 MET C 1
REMARK 465 ARG C 2
REMARK 465 SER C 3
REMARK 465 ARG C 4
REMARK 465 ARG C 5
REMARK 465 VAL C 6
REMARK 465 ASP C 7
REMARK 465 LEU C 226
REMARK 465 ASN C 227
REMARK 465 PRO C 228
REMARK 465 MET D 1
REMARK 465 ARG D 2
REMARK 465 SER D 3
REMARK 465 ARG D 4
REMARK 465 ARG D 5
REMARK 465 VAL D 6
REMARK 465 ASP D 7
REMARK 465 VAL D 8
REMARK 465 LEU D 226
REMARK 465 ASN D 227
REMARK 465 PRO D 228
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 ASN A 13 17.66 55.89
REMARK 500 LYS A 72 53.55 34.15
REMARK 500 ALA A 74 49.84 -144.59
REMARK 500 THR A 124 -93.20 -94.15
REMARK 500 PHE A 134 -41.61 -132.20
REMARK 500 ASN B 13 18.42 57.65
REMARK 500 LYS B 72 48.25 39.58
REMARK 500 ALA B 74 48.07 -146.70
REMARK 500 THR B 124 -85.56 -94.51
REMARK 500 ASN C 13 18.92 57.17
REMARK 500 LYS C 72 53.44 33.63
REMARK 500 ALA C 74 50.29 -145.13
REMARK 500 THR C 124 -93.55 -93.46
REMARK 500 PHE C 134 -41.81 -131.13
REMARK 500 ASN D 13 19.15 56.74
REMARK 500 LYS D 72 48.76 39.38
REMARK 500 ALA D 74 47.41 -146.71
REMARK 500 THR D 124 -84.95 -94.81
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMQ A 229
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMQ B 229
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMQ C 229
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMQ D 229
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3LHT RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT V201F OF OROTIDINE 5'-MONOPHOSPHATE
REMARK 900 DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED
REMARK 900 WITH INHIBITOR BMP
REMARK 900 RELATED ID: 3LHU RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT I199F OF OROTIDINE 5'-MONOPHOSPHATE
REMARK 900 DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED
REMARK 900 WITH INHIBITOR BMP
REMARK 900 RELATED ID: 3LHW RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT V182A OF OROTIDINE 5'-MONOPHOSPHATE
REMARK 900 DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED
REMARK 900 WITH INHIBITOR BMP
REMARK 900 RELATED ID: 3LHY RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT I199A OF OROTIDINE 5'-MONOPHOSPHATE
REMARK 900 DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED
REMARK 900 WITH INHIBITOR BMP
REMARK 900 RELATED ID: 3LHZ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT V201A OF OROTIDINE 5'-MONOPHOSPHATE
REMARK 900 DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED
REMARK 900 WITH INHIBITOR BMP
REMARK 900 RELATED ID: 3LI0 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT R203A OF OROTIDINE 5'-MONOPHOSPHATE
REMARK 900 DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED
REMARK 900 WITH INHIBITOR BMP
REMARK 900 RELATED ID: 3LI1 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE MUTANT I218A OF OROTIDINE 5'-MONOPHOSPHATE
REMARK 900 DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED
REMARK 900 WITH INHIBITOR BMP
DBREF 3LHV A 1 228 UNP O26232 PYRF_METTH 1 228
DBREF 3LHV B 1 228 UNP O26232 PYRF_METTH 1 228
DBREF 3LHV C 1 228 UNP O26232 PYRF_METTH 1 228
DBREF 3LHV D 1 228 UNP O26232 PYRF_METTH 1 228
SEQADV 3LHV PRO A 101 UNP O26232 ARG 101 ENGINEERED MUTATION
SEQADV 3LHV ALA A 182 UNP O26232 VAL 182 ENGINEERED MUTATION
SEQADV 3LHV ALA A 199 UNP O26232 ILE 199 ENGINEERED MUTATION
SEQADV 3LHV ALA A 201 UNP O26232 VAL 201 ENGINEERED MUTATION
SEQADV 3LHV PRO B 101 UNP O26232 ARG 101 ENGINEERED MUTATION
SEQADV 3LHV ALA B 182 UNP O26232 VAL 182 ENGINEERED MUTATION
SEQADV 3LHV ALA B 199 UNP O26232 ILE 199 ENGINEERED MUTATION
SEQADV 3LHV ALA B 201 UNP O26232 VAL 201 ENGINEERED MUTATION
SEQADV 3LHV PRO C 101 UNP O26232 ARG 101 ENGINEERED MUTATION
SEQADV 3LHV ALA C 182 UNP O26232 VAL 182 ENGINEERED MUTATION
SEQADV 3LHV ALA C 199 UNP O26232 ILE 199 ENGINEERED MUTATION
SEQADV 3LHV ALA C 201 UNP O26232 VAL 201 ENGINEERED MUTATION
SEQADV 3LHV PRO D 101 UNP O26232 ARG 101 ENGINEERED MUTATION
SEQADV 3LHV ALA D 182 UNP O26232 VAL 182 ENGINEERED MUTATION
SEQADV 3LHV ALA D 199 UNP O26232 ILE 199 ENGINEERED MUTATION
SEQADV 3LHV ALA D 201 UNP O26232 VAL 201 ENGINEERED MUTATION
SEQRES 1 A 228 MET ARG SER ARG ARG VAL ASP VAL MET ASP VAL MET ASN
SEQRES 2 A 228 ARG LEU ILE LEU ALA MET ASP LEU MET ASN ARG ASP ASP
SEQRES 3 A 228 ALA LEU ARG VAL THR GLY GLU VAL ARG GLU TYR ILE ASP
SEQRES 4 A 228 THR VAL LYS ILE GLY TYR PRO LEU VAL LEU SER GLU GLY
SEQRES 5 A 228 MET ASP ILE ILE ALA GLU PHE ARG LYS ARG PHE GLY CYS
SEQRES 6 A 228 ARG ILE ILE ALA ASP PHE LYS VAL ALA ASP ILE PRO GLU
SEQRES 7 A 228 THR ASN GLU LYS ILE CYS ARG ALA THR PHE LYS ALA GLY
SEQRES 8 A 228 ALA ASP ALA ILE ILE VAL HIS GLY PHE PRO GLY ALA ASP
SEQRES 9 A 228 SER VAL ARG ALA CYS LEU ASN VAL ALA GLU GLU MET GLY
SEQRES 10 A 228 ARG GLU VAL PHE LEU LEU THR GLU MET SER HIS PRO GLY
SEQRES 11 A 228 ALA GLU MET PHE ILE GLN GLY ALA ALA ASP GLU ILE ALA
SEQRES 12 A 228 ARG MET GLY VAL ASP LEU GLY VAL LYS ASN TYR VAL GLY
SEQRES 13 A 228 PRO SER THR ARG PRO GLU ARG LEU SER ARG LEU ARG GLU
SEQRES 14 A 228 ILE ILE GLY GLN ASP SER PHE LEU ILE SER PRO GLY ALA
SEQRES 15 A 228 GLY ALA GLN GLY GLY ASP PRO GLY GLU THR LEU ARG PHE
SEQRES 16 A 228 ALA ASP ALA ALA ILE ALA GLY ARG SER ILE TYR LEU ALA
SEQRES 17 A 228 ASP ASN PRO ALA ALA ALA ALA ALA GLY ILE ILE GLU SER
SEQRES 18 A 228 ILE LYS ASP LEU LEU ASN PRO
SEQRES 1 B 228 MET ARG SER ARG ARG VAL ASP VAL MET ASP VAL MET ASN
SEQRES 2 B 228 ARG LEU ILE LEU ALA MET ASP LEU MET ASN ARG ASP ASP
SEQRES 3 B 228 ALA LEU ARG VAL THR GLY GLU VAL ARG GLU TYR ILE ASP
SEQRES 4 B 228 THR VAL LYS ILE GLY TYR PRO LEU VAL LEU SER GLU GLY
SEQRES 5 B 228 MET ASP ILE ILE ALA GLU PHE ARG LYS ARG PHE GLY CYS
SEQRES 6 B 228 ARG ILE ILE ALA ASP PHE LYS VAL ALA ASP ILE PRO GLU
SEQRES 7 B 228 THR ASN GLU LYS ILE CYS ARG ALA THR PHE LYS ALA GLY
SEQRES 8 B 228 ALA ASP ALA ILE ILE VAL HIS GLY PHE PRO GLY ALA ASP
SEQRES 9 B 228 SER VAL ARG ALA CYS LEU ASN VAL ALA GLU GLU MET GLY
SEQRES 10 B 228 ARG GLU VAL PHE LEU LEU THR GLU MET SER HIS PRO GLY
SEQRES 11 B 228 ALA GLU MET PHE ILE GLN GLY ALA ALA ASP GLU ILE ALA
SEQRES 12 B 228 ARG MET GLY VAL ASP LEU GLY VAL LYS ASN TYR VAL GLY
SEQRES 13 B 228 PRO SER THR ARG PRO GLU ARG LEU SER ARG LEU ARG GLU
SEQRES 14 B 228 ILE ILE GLY GLN ASP SER PHE LEU ILE SER PRO GLY ALA
SEQRES 15 B 228 GLY ALA GLN GLY GLY ASP PRO GLY GLU THR LEU ARG PHE
SEQRES 16 B 228 ALA ASP ALA ALA ILE ALA GLY ARG SER ILE TYR LEU ALA
SEQRES 17 B 228 ASP ASN PRO ALA ALA ALA ALA ALA GLY ILE ILE GLU SER
SEQRES 18 B 228 ILE LYS ASP LEU LEU ASN PRO
SEQRES 1 C 228 MET ARG SER ARG ARG VAL ASP VAL MET ASP VAL MET ASN
SEQRES 2 C 228 ARG LEU ILE LEU ALA MET ASP LEU MET ASN ARG ASP ASP
SEQRES 3 C 228 ALA LEU ARG VAL THR GLY GLU VAL ARG GLU TYR ILE ASP
SEQRES 4 C 228 THR VAL LYS ILE GLY TYR PRO LEU VAL LEU SER GLU GLY
SEQRES 5 C 228 MET ASP ILE ILE ALA GLU PHE ARG LYS ARG PHE GLY CYS
SEQRES 6 C 228 ARG ILE ILE ALA ASP PHE LYS VAL ALA ASP ILE PRO GLU
SEQRES 7 C 228 THR ASN GLU LYS ILE CYS ARG ALA THR PHE LYS ALA GLY
SEQRES 8 C 228 ALA ASP ALA ILE ILE VAL HIS GLY PHE PRO GLY ALA ASP
SEQRES 9 C 228 SER VAL ARG ALA CYS LEU ASN VAL ALA GLU GLU MET GLY
SEQRES 10 C 228 ARG GLU VAL PHE LEU LEU THR GLU MET SER HIS PRO GLY
SEQRES 11 C 228 ALA GLU MET PHE ILE GLN GLY ALA ALA ASP GLU ILE ALA
SEQRES 12 C 228 ARG MET GLY VAL ASP LEU GLY VAL LYS ASN TYR VAL GLY
SEQRES 13 C 228 PRO SER THR ARG PRO GLU ARG LEU SER ARG LEU ARG GLU
SEQRES 14 C 228 ILE ILE GLY GLN ASP SER PHE LEU ILE SER PRO GLY ALA
SEQRES 15 C 228 GLY ALA GLN GLY GLY ASP PRO GLY GLU THR LEU ARG PHE
SEQRES 16 C 228 ALA ASP ALA ALA ILE ALA GLY ARG SER ILE TYR LEU ALA
SEQRES 17 C 228 ASP ASN PRO ALA ALA ALA ALA ALA GLY ILE ILE GLU SER
SEQRES 18 C 228 ILE LYS ASP LEU LEU ASN PRO
SEQRES 1 D 228 MET ARG SER ARG ARG VAL ASP VAL MET ASP VAL MET ASN
SEQRES 2 D 228 ARG LEU ILE LEU ALA MET ASP LEU MET ASN ARG ASP ASP
SEQRES 3 D 228 ALA LEU ARG VAL THR GLY GLU VAL ARG GLU TYR ILE ASP
SEQRES 4 D 228 THR VAL LYS ILE GLY TYR PRO LEU VAL LEU SER GLU GLY
SEQRES 5 D 228 MET ASP ILE ILE ALA GLU PHE ARG LYS ARG PHE GLY CYS
SEQRES 6 D 228 ARG ILE ILE ALA ASP PHE LYS VAL ALA ASP ILE PRO GLU
SEQRES 7 D 228 THR ASN GLU LYS ILE CYS ARG ALA THR PHE LYS ALA GLY
SEQRES 8 D 228 ALA ASP ALA ILE ILE VAL HIS GLY PHE PRO GLY ALA ASP
SEQRES 9 D 228 SER VAL ARG ALA CYS LEU ASN VAL ALA GLU GLU MET GLY
SEQRES 10 D 228 ARG GLU VAL PHE LEU LEU THR GLU MET SER HIS PRO GLY
SEQRES 11 D 228 ALA GLU MET PHE ILE GLN GLY ALA ALA ASP GLU ILE ALA
SEQRES 12 D 228 ARG MET GLY VAL ASP LEU GLY VAL LYS ASN TYR VAL GLY
SEQRES 13 D 228 PRO SER THR ARG PRO GLU ARG LEU SER ARG LEU ARG GLU
SEQRES 14 D 228 ILE ILE GLY GLN ASP SER PHE LEU ILE SER PRO GLY ALA
SEQRES 15 D 228 GLY ALA GLN GLY GLY ASP PRO GLY GLU THR LEU ARG PHE
SEQRES 16 D 228 ALA ASP ALA ALA ILE ALA GLY ARG SER ILE TYR LEU ALA
SEQRES 17 D 228 ASP ASN PRO ALA ALA ALA ALA ALA GLY ILE ILE GLU SER
SEQRES 18 D 228 ILE LYS ASP LEU LEU ASN PRO
HET BMQ A 229 22
HET BMQ B 229 22
HET BMQ C 229 22
HET BMQ D 229 22
HETNAM BMQ 1-(5'-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID
FORMUL 5 BMQ 4(C9 H13 N2 O10 P)
FORMUL 9 HOH *580(H2 O)
HELIX 1 1 VAL A 11 ASN A 13 5 3
HELIX 2 2 ASN A 23 ARG A 35 1 13
HELIX 3 3 TYR A 45 GLY A 52 1 8
HELIX 4 4 MET A 53 GLY A 64 1 12
HELIX 5 5 ILE A 76 ALA A 90 1 15
HELIX 6 6 GLY A 102 GLY A 117 1 16
HELIX 7 7 HIS A 128 MET A 133 5 6
HELIX 8 8 PHE A 134 GLY A 150 1 17
HELIX 9 9 ARG A 160 GLY A 172 1 13
HELIX 10 10 ASP A 188 LEU A 193 1 6
HELIX 11 11 GLY A 202 LEU A 207 1 6
HELIX 12 12 ASN A 210 SER A 221 1 12
HELIX 13 13 VAL B 11 ASN B 13 5 3
HELIX 14 14 ASN B 23 VAL B 34 1 12
HELIX 15 15 TYR B 45 GLY B 52 1 8
HELIX 16 16 MET B 53 GLY B 64 1 12
HELIX 17 17 ILE B 76 ALA B 90 1 15
HELIX 18 18 GLY B 102 GLY B 117 1 16
HELIX 19 19 HIS B 128 MET B 133 5 6
HELIX 20 20 PHE B 134 GLY B 150 1 17
HELIX 21 21 ARG B 160 GLY B 172 1 13
HELIX 22 22 ASP B 188 LEU B 193 1 6
HELIX 23 23 GLY B 202 LEU B 207 1 6
HELIX 24 24 ASN B 210 ILE B 222 1 13
HELIX 25 25 VAL C 11 ASN C 13 5 3
HELIX 26 26 ASN C 23 ARG C 35 1 13
HELIX 27 27 TYR C 45 GLY C 52 1 8
HELIX 28 28 MET C 53 GLY C 64 1 12
HELIX 29 29 ILE C 76 ALA C 90 1 15
HELIX 30 30 GLY C 102 GLY C 117 1 16
HELIX 31 31 HIS C 128 MET C 133 5 6
HELIX 32 32 PHE C 134 GLY C 150 1 17
HELIX 33 33 ARG C 160 GLY C 172 1 13
HELIX 34 34 ASP C 188 LEU C 193 1 6
HELIX 35 35 GLY C 202 LEU C 207 1 6
HELIX 36 36 ASN C 210 SER C 221 1 12
HELIX 37 37 VAL D 11 ASN D 13 5 3
HELIX 38 38 ASN D 23 VAL D 34 1 12
HELIX 39 39 TYR D 45 GLY D 52 1 8
HELIX 40 40 MET D 53 GLY D 64 1 12
HELIX 41 41 ILE D 76 ALA D 90 1 15
HELIX 42 42 GLY D 102 GLY D 117 1 16
HELIX 43 43 HIS D 128 MET D 133 5 6
HELIX 44 44 PHE D 134 GLY D 150 1 17
HELIX 45 45 ARG D 160 GLY D 172 1 13
HELIX 46 46 ASP D 188 LEU D 193 1 6
HELIX 47 47 GLY D 202 LEU D 207 1 6
HELIX 48 48 ASN D 210 ILE D 222 1 13
SHEET 1 A 9 LEU A 15 MET A 19 0
SHEET 2 A 9 THR A 40 GLY A 44 1 O LYS A 42 N LEU A 17
SHEET 3 A 9 ARG A 66 VAL A 73 1 O ARG A 66 N VAL A 41
SHEET 4 A 9 ALA A 94 HIS A 98 1 O ALA A 94 N ALA A 69
SHEET 5 A 9 GLU A 119 LEU A 123 1 O PHE A 121 N VAL A 97
SHEET 6 A 9 ASN A 153 VAL A 155 1 O ASN A 153 N LEU A 122
SHEET 7 A 9 PHE A 176 SER A 179 1 O PHE A 176 N TYR A 154
SHEET 8 A 9 ALA A 198 ALA A 201 1 O ILE A 200 N SER A 179
SHEET 9 A 9 LEU A 15 MET A 19 1 N ILE A 16 O ALA A 199
SHEET 1 B 9 LEU B 15 MET B 19 0
SHEET 2 B 9 THR B 40 GLY B 44 1 O LYS B 42 N LEU B 17
SHEET 3 B 9 ARG B 66 VAL B 73 1 O ARG B 66 N VAL B 41
SHEET 4 B 9 ALA B 94 HIS B 98 1 O ALA B 94 N ALA B 69
SHEET 5 B 9 GLU B 119 LEU B 123 1 O PHE B 121 N VAL B 97
SHEET 6 B 9 ASN B 153 VAL B 155 1 O ASN B 153 N LEU B 122
SHEET 7 B 9 PHE B 176 SER B 179 1 O PHE B 176 N TYR B 154
SHEET 8 B 9 ALA B 198 ALA B 201 1 O ILE B 200 N SER B 179
SHEET 9 B 9 LEU B 15 MET B 19 1 N ILE B 16 O ALA B 199
SHEET 1 C 9 LEU C 15 MET C 19 0
SHEET 2 C 9 THR C 40 GLY C 44 1 O LYS C 42 N LEU C 17
SHEET 3 C 9 ARG C 66 VAL C 73 1 O ARG C 66 N VAL C 41
SHEET 4 C 9 ALA C 94 HIS C 98 1 O ALA C 94 N ALA C 69
SHEET 5 C 9 GLU C 119 LEU C 123 1 O PHE C 121 N VAL C 97
SHEET 6 C 9 ASN C 153 VAL C 155 1 O ASN C 153 N LEU C 122
SHEET 7 C 9 PHE C 176 SER C 179 1 O PHE C 176 N TYR C 154
SHEET 8 C 9 ALA C 198 ALA C 201 1 O ILE C 200 N SER C 179
SHEET 9 C 9 LEU C 15 MET C 19 1 N ILE C 16 O ALA C 199
SHEET 1 D 9 LEU D 15 MET D 19 0
SHEET 2 D 9 THR D 40 GLY D 44 1 O LYS D 42 N LEU D 17
SHEET 3 D 9 ARG D 66 VAL D 73 1 O ARG D 66 N VAL D 41
SHEET 4 D 9 ALA D 94 HIS D 98 1 O ALA D 94 N ALA D 69
SHEET 5 D 9 GLU D 119 LEU D 123 1 O PHE D 121 N VAL D 97
SHEET 6 D 9 ASN D 153 VAL D 155 1 O ASN D 153 N LEU D 122
SHEET 7 D 9 PHE D 176 SER D 179 1 O PHE D 176 N TYR D 154
SHEET 8 D 9 ALA D 198 ALA D 201 1 O ILE D 200 N SER D 179
SHEET 9 D 9 LEU D 15 MET D 19 1 N ILE D 16 O ALA D 199
SITE 1 AC1 20 ASP A 20 LYS A 42 ASP A 70 LYS A 72
SITE 2 AC1 20 MET A 126 SER A 127 PRO A 180 GLN A 185
SITE 3 AC1 20 GLY A 202 ARG A 203 HOH A 238 HOH A 240
SITE 4 AC1 20 HOH A 241 HOH A 244 HOH A 245 HOH A 247
SITE 5 AC1 20 HOH A 248 ASP B 75 ILE B 76 THR B 79
SITE 1 AC2 20 ASP A 75 ILE A 76 THR A 79 ASP B 20
SITE 2 AC2 20 LYS B 42 ASP B 70 LYS B 72 MET B 126
SITE 3 AC2 20 SER B 127 PRO B 180 GLN B 185 GLY B 202
SITE 4 AC2 20 ARG B 203 HOH B 239 HOH B 244 HOH B 246
SITE 5 AC2 20 HOH B 247 HOH B 249 HOH B 251 HOH B 271
SITE 1 AC3 20 ASP C 20 LYS C 42 ASP C 70 LYS C 72
SITE 2 AC3 20 MET C 126 SER C 127 PRO C 180 GLN C 185
SITE 3 AC3 20 GLY C 202 ARG C 203 HOH C 238 HOH C 241
SITE 4 AC3 20 HOH C 242 HOH C 244 HOH C 246 HOH C 248
SITE 5 AC3 20 HOH C 250 ASP D 75 ILE D 76 THR D 79
SITE 1 AC4 20 ASP C 75 ILE C 76 THR C 79 ASP D 20
SITE 2 AC4 20 LYS D 42 ASP D 70 LYS D 72 MET D 126
SITE 3 AC4 20 SER D 127 PRO D 180 GLN D 185 GLY D 202
SITE 4 AC4 20 ARG D 203 HOH D 236 HOH D 241 HOH D 244
SITE 5 AC4 20 HOH D 248 HOH D 249 HOH D 251 HOH D 285
CRYST1 64.789 64.162 102.427 90.00 91.99 90.00 P 1 21 1 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 0.015435 0.000000 0.000536 0.00000
SCALE2 0.000000 0.015586 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009769 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
