HEADER LYASE 05-DEC-07 3BK0
TITLE CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
TITLE 2 COMPLEXED WITH 5-CN-UMP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: URIDINE 5'-MONOPHOSPHATE SYNTHASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: UMP SYNTHASE, OROTIDINE 5'-PHOSPHATE DECARBOXYLASE,
COMPND 5 OMPDECASE;
COMPND 6 EC: 4.1.1.23;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: UMPS;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS UMP SYNTHASE, C-TERMINAL DOMAIN, OROTIDINE 5'-MONOPHOSPHATE
KEYWDS 2 DECARBOXYLASE, HUMAN, 5-CN-UMP, DISEASE MUTATION,
KEYWDS 3 GLYCOSYLTRANSFERASE, LYASE, MULTIFUNCTIONAL ENZYME, PYRIMIDINE
KEYWDS 4 BIOSYNTHESIS, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.LIU,H.L.TANG,M.E.M.AVINA,L.P.KOTRA,E.F.PAI
REVDAT 4 30-AUG-23 3BK0 1 REMARK SEQADV
REVDAT 3 13-JUL-11 3BK0 1 VERSN
REVDAT 2 24-FEB-09 3BK0 1 VERSN
REVDAT 1 18-NOV-08 3BK0 0
JRNL AUTH Y.LIU,H.L.TANG,M.E.M.AVINA,L.P.KOTRA,E.F.PAI
JRNL TITL CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE
JRNL TITL 2 DECARBOXYLASE COMPLEXED WITH 5-CN-UMP
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.60 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 78.3
REMARK 3 NUMBER OF REFLECTIONS : 55585
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.181
REMARK 3 R VALUE (WORKING SET) : 0.179
REMARK 3 FREE R VALUE : 0.216
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2938
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.63
REMARK 3 REFLECTION IN BIN (WORKING SET) : 969
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 18.57
REMARK 3 BIN R VALUE (WORKING SET) : 0.2750
REMARK 3 BIN FREE R VALUE SET COUNT : 49
REMARK 3 BIN FREE R VALUE : 0.3370
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 : 68
REMARK 3 SOLVENT ATOMS : 256
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.35
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.60000
REMARK 3 B22 (A**2) : -1.27000
REMARK 3 B33 (A**2) : 2.05000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 1.85000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.109
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.785
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4325 ; 0.010 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5880 ; 1.514 ; 1.992
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 571 ; 6.039 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;36.328 ;23.873
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 780 ;12.790 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;16.749 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 664 ; 0.100 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3236 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2191 ; 0.211 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3093 ; 0.307 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 325 ; 0.134 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 44 ; 0.250 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.168 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2810 ; 0.969 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4385 ; 1.486 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1701 ; 2.475 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1495 ; 3.951 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3BK0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-07.
REMARK 100 THE DEPOSITION ID IS D_1000045614.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-AUG-07
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : CLSI
REMARK 200 BEAMLINE : 08ID-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : DCM WITH CRYO-COOLED 1ST CRYSTAL
REMARK 200 SAGITTALLY BENT 2ND CRYSTAL
REMARK 200 FOLLOWED BY VERTICALLY FOCUSING
REMARK 200 MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58523
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 78.5
REMARK 200 DATA REDUNDANCY : 3.300
REMARK 200 R MERGE (I) : 0.05800
REMARK 200 R SYM (I) : 0.05800
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000
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) : 1.66
REMARK 200 COMPLETENESS FOR SHELL (%) : 21.7
REMARK 200 DATA REDUNDANCY IN SHELL : 1.70
REMARK 200 R MERGE FOR SHELL (I) : 0.32300
REMARK 200 R SYM FOR SHELL (I) : 0.32300
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.950
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 2P1F
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.87
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 8.4, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K
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 30.77700
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4600 ANGSTROM**2
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 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 13
REMARK 465 GLY A 14
REMARK 465 SER A 15
REMARK 465 SER A 16
REMARK 465 HIS A 17
REMARK 465 HIS A 18
REMARK 465 HIS A 19
REMARK 465 HIS A 20
REMARK 465 HIS A 21
REMARK 465 HIS A 22
REMARK 465 SER A 23
REMARK 465 SER A 24
REMARK 465 GLY A 25
REMARK 465 LEU A 26
REMARK 465 VAL A 27
REMARK 465 PRO A 28
REMARK 465 ARG A 29
REMARK 465 GLY A 30
REMARK 465 SER A 31
REMARK 465 HIS A 32
REMARK 465 MET A 33
REMARK 465 VAL A 291
REMARK 465 MET B 13
REMARK 465 GLY B 14
REMARK 465 SER B 15
REMARK 465 SER B 16
REMARK 465 HIS B 17
REMARK 465 HIS B 18
REMARK 465 HIS B 19
REMARK 465 HIS B 20
REMARK 465 HIS B 21
REMARK 465 HIS B 22
REMARK 465 SER B 23
REMARK 465 SER B 24
REMARK 465 GLY B 25
REMARK 465 LEU B 26
REMARK 465 VAL B 27
REMARK 465 PRO B 28
REMARK 465 ARG B 29
REMARK 465 GLY B 30
REMARK 465 SER B 31
REMARK 465 HIS B 32
REMARK 465 MET B 33
REMARK 465 VAL B 291
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 ALA A 69 71.64 -103.02
REMARK 500 GLU A 117 73.80 68.37
REMARK 500 ALA A 127 42.42 -158.53
REMARK 500 TRP A 147 -16.25 -151.53
REMARK 500 PHE A 207 -36.83 -130.24
REMARK 500 GLU B 117 73.75 64.40
REMARK 500 ALA B 127 45.33 -157.68
REMARK 500 PHE B 207 -36.54 -131.65
REMARK 500 ASP B 237 -166.18 -111.03
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 SO4 A 3001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CNU A 1000
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CNU B 1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2000
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2001
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2EAW RELATED DB: PDB
REMARK 900 HUMAN UMP SYNTHASE(C-TERMINAL DOMAIN-OROTIDINE 5'-MONOPHOSPHATE
REMARK 900 DECARBOXYLASE)
REMARK 900 RELATED ID: 2P1F RELATED DB: PDB
REMARK 900 HUMAN UMP SYNTHASE(C-TERMINAL DOMAIN-OROTIDINE 5'-MONOPHOSPHATE
REMARK 900 DECARBOXYLASE)
REMARK 900 RELATED ID: 3BGG RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
REMARK 900 COMPLEXED WITH BMP
REMARK 900 RELATED ID: 3BGJ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
REMARK 900 COVALENTLY MODIFIED BY 6-IODO-UMP
REMARK 900 RELATED ID: 3BVJ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
REMARK 900 COMPLEXED WITH XMP
DBREF 3BK0 A 34 291 UNP P11172 PYR5_HUMAN 223 480
DBREF 3BK0 B 34 291 UNP P11172 PYR5_HUMAN 223 480
SEQADV 3BK0 MET A 13 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 GLY A 14 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 SER A 15 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 SER A 16 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS A 17 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS A 18 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS A 19 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS A 20 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS A 21 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS A 22 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 SER A 23 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 SER A 24 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 GLY A 25 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 LEU A 26 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 VAL A 27 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 PRO A 28 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 ARG A 29 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 GLY A 30 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 SER A 31 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS A 32 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 MET A 33 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 MET B 13 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 GLY B 14 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 SER B 15 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 SER B 16 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS B 17 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS B 18 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS B 19 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS B 20 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS B 21 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS B 22 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 SER B 23 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 SER B 24 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 GLY B 25 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 LEU B 26 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 VAL B 27 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 PRO B 28 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 ARG B 29 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 GLY B 30 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 SER B 31 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 HIS B 32 UNP P11172 EXPRESSION TAG
SEQADV 3BK0 MET B 33 UNP P11172 EXPRESSION TAG
SEQRES 1 A 279 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES 2 A 279 LEU VAL PRO ARG GLY SER HIS MET LYS GLU LEU SER PHE
SEQRES 3 A 279 GLY ALA ARG ALA GLU LEU PRO ARG ILE HIS PRO VAL ALA
SEQRES 4 A 279 SER LYS LEU LEU ARG LEU MET GLN LYS LYS GLU THR ASN
SEQRES 5 A 279 LEU CYS LEU SER ALA ASP VAL SER LEU ALA ARG GLU LEU
SEQRES 6 A 279 LEU GLN LEU ALA ASP ALA LEU GLY PRO SER ILE CYS MET
SEQRES 7 A 279 LEU LYS THR HIS VAL ASP ILE LEU ASN ASP PHE THR LEU
SEQRES 8 A 279 ASP VAL MET LYS GLU LEU ILE THR LEU ALA LYS CYS HIS
SEQRES 9 A 279 GLU PHE LEU ILE PHE GLU ASP ARG LYS PHE ALA ASP ILE
SEQRES 10 A 279 GLY ASN THR VAL LYS LYS GLN TYR GLU GLY GLY ILE PHE
SEQRES 11 A 279 LYS ILE ALA SER TRP ALA ASP LEU VAL ASN ALA HIS VAL
SEQRES 12 A 279 VAL PRO GLY SER GLY VAL VAL LYS GLY LEU GLN GLU VAL
SEQRES 13 A 279 GLY LEU PRO LEU HIS ARG GLY CYS LEU LEU ILE ALA GLU
SEQRES 14 A 279 MET SER SER THR GLY SER LEU ALA THR GLY ASP TYR THR
SEQRES 15 A 279 ARG ALA ALA VAL ARG MET ALA GLU GLU HIS SER GLU PHE
SEQRES 16 A 279 VAL VAL GLY PHE ILE SER GLY SER ARG VAL SER MET LYS
SEQRES 17 A 279 PRO GLU PHE LEU HIS LEU THR PRO GLY VAL GLN LEU GLU
SEQRES 18 A 279 ALA GLY GLY ASP ASN LEU GLY GLN GLN TYR ASN SER PRO
SEQRES 19 A 279 GLN GLU VAL ILE GLY LYS ARG GLY SER ASP ILE ILE ILE
SEQRES 20 A 279 VAL GLY ARG GLY ILE ILE SER ALA ALA ASP ARG LEU GLU
SEQRES 21 A 279 ALA ALA GLU MET TYR ARG LYS ALA ALA TRP GLU ALA TYR
SEQRES 22 A 279 LEU SER ARG LEU GLY VAL
SEQRES 1 B 279 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES 2 B 279 LEU VAL PRO ARG GLY SER HIS MET LYS GLU LEU SER PHE
SEQRES 3 B 279 GLY ALA ARG ALA GLU LEU PRO ARG ILE HIS PRO VAL ALA
SEQRES 4 B 279 SER LYS LEU LEU ARG LEU MET GLN LYS LYS GLU THR ASN
SEQRES 5 B 279 LEU CYS LEU SER ALA ASP VAL SER LEU ALA ARG GLU LEU
SEQRES 6 B 279 LEU GLN LEU ALA ASP ALA LEU GLY PRO SER ILE CYS MET
SEQRES 7 B 279 LEU LYS THR HIS VAL ASP ILE LEU ASN ASP PHE THR LEU
SEQRES 8 B 279 ASP VAL MET LYS GLU LEU ILE THR LEU ALA LYS CYS HIS
SEQRES 9 B 279 GLU PHE LEU ILE PHE GLU ASP ARG LYS PHE ALA ASP ILE
SEQRES 10 B 279 GLY ASN THR VAL LYS LYS GLN TYR GLU GLY GLY ILE PHE
SEQRES 11 B 279 LYS ILE ALA SER TRP ALA ASP LEU VAL ASN ALA HIS VAL
SEQRES 12 B 279 VAL PRO GLY SER GLY VAL VAL LYS GLY LEU GLN GLU VAL
SEQRES 13 B 279 GLY LEU PRO LEU HIS ARG GLY CYS LEU LEU ILE ALA GLU
SEQRES 14 B 279 MET SER SER THR GLY SER LEU ALA THR GLY ASP TYR THR
SEQRES 15 B 279 ARG ALA ALA VAL ARG MET ALA GLU GLU HIS SER GLU PHE
SEQRES 16 B 279 VAL VAL GLY PHE ILE SER GLY SER ARG VAL SER MET LYS
SEQRES 17 B 279 PRO GLU PHE LEU HIS LEU THR PRO GLY VAL GLN LEU GLU
SEQRES 18 B 279 ALA GLY GLY ASP ASN LEU GLY GLN GLN TYR ASN SER PRO
SEQRES 19 B 279 GLN GLU VAL ILE GLY LYS ARG GLY SER ASP ILE ILE ILE
SEQRES 20 B 279 VAL GLY ARG GLY ILE ILE SER ALA ALA ASP ARG LEU GLU
SEQRES 21 B 279 ALA ALA GLU MET TYR ARG LYS ALA ALA TRP GLU ALA TYR
SEQRES 22 B 279 LEU SER ARG LEU GLY VAL
HET SO4 A3000 5
HET SO4 A3001 5
HET CNU A1000 23
HET GOL A2000 6
HET GOL A2001 6
HET CNU B1001 23
HETNAM SO4 SULFATE ION
HETNAM CNU 5-CYANO-URIDINE-5'-MONOPHOSPHATE
HETNAM GOL GLYCEROL
HETSYN CNU 5-CYANO-UMP; 5-CYANOURIDINE 5'-(DIHYDROGEN PHOSPHATE)
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 SO4 2(O4 S 2-)
FORMUL 5 CNU 2(C10 H12 N3 O9 P)
FORMUL 6 GOL 2(C3 H8 O3)
FORMUL 9 HOH *256(H2 O)
HELIX 1 1 SER A 37 ALA A 42 1 6
HELIX 2 2 HIS A 48 GLU A 62 1 15
HELIX 3 3 LEU A 73 GLY A 85 1 13
HELIX 4 4 PRO A 86 ILE A 88 5 3
HELIX 5 5 HIS A 94 LEU A 98 5 5
HELIX 6 6 THR A 102 GLU A 117 1 16
HELIX 7 7 ILE A 129 GLY A 139 1 11
HELIX 8 8 LYS A 143 TRP A 147 5 5
HELIX 9 9 SER A 159 LEU A 170 1 12
HELIX 10 10 GLY A 191 GLU A 203 1 13
HELIX 11 11 SER A 245 LYS A 252 1 8
HELIX 12 12 GLY A 261 SER A 266 1 6
HELIX 13 13 ASP A 269 GLY A 290 1 22
HELIX 14 14 SER B 37 ALA B 42 1 6
HELIX 15 15 HIS B 48 GLU B 62 1 15
HELIX 16 16 LEU B 73 GLY B 85 1 13
HELIX 17 17 PRO B 86 ILE B 88 5 3
HELIX 18 18 HIS B 94 LEU B 98 5 5
HELIX 19 19 THR B 102 GLU B 117 1 16
HELIX 20 20 ILE B 129 GLY B 139 1 11
HELIX 21 21 LYS B 143 TRP B 147 5 5
HELIX 22 22 SER B 159 LEU B 170 1 12
HELIX 23 23 THR B 190 HIS B 204 1 15
HELIX 24 24 SER B 245 LYS B 252 1 8
HELIX 25 25 GLY B 261 SER B 266 1 6
HELIX 26 26 ASP B 269 GLY B 290 1 22
SHEET 1 A 9 LEU A 65 SER A 68 0
SHEET 2 A 9 MET A 90 THR A 93 1 O LYS A 92 N LEU A 67
SHEET 3 A 9 LEU A 119 PHE A 126 1 O PHE A 121 N LEU A 91
SHEET 4 A 9 LEU A 150 HIS A 154 1 O HIS A 154 N PHE A 126
SHEET 5 A 9 GLY A 175 ILE A 179 1 O LEU A 177 N VAL A 151
SHEET 6 A 9 VAL A 208 ILE A 212 1 O VAL A 209 N CYS A 176
SHEET 7 A 9 LEU A 224 THR A 227 1 O LEU A 224 N PHE A 211
SHEET 8 A 9 ILE A 257 VAL A 260 1 O ILE A 259 N THR A 227
SHEET 9 A 9 LEU A 65 SER A 68 1 N CYS A 66 O ILE A 258
SHEET 1 B 2 GLY A 235 GLY A 236 0
SHEET 2 B 2 GLN A 242 TYR A 243 -1 O TYR A 243 N GLY A 235
SHEET 1 C 9 LEU B 65 SER B 68 0
SHEET 2 C 9 MET B 90 THR B 93 1 O LYS B 92 N LEU B 67
SHEET 3 C 9 LEU B 119 PHE B 126 1 O PHE B 121 N LEU B 91
SHEET 4 C 9 LEU B 150 HIS B 154 1 O HIS B 154 N PHE B 126
SHEET 5 C 9 GLY B 175 ILE B 179 1 O ILE B 179 N ALA B 153
SHEET 6 C 9 VAL B 208 ILE B 212 1 O VAL B 209 N CYS B 176
SHEET 7 C 9 LEU B 224 THR B 227 1 O LEU B 224 N PHE B 211
SHEET 8 C 9 ILE B 257 VAL B 260 1 O ILE B 257 N THR B 227
SHEET 9 C 9 LEU B 65 SER B 68 1 N CYS B 66 O ILE B 258
SHEET 1 D 2 GLY B 235 GLY B 236 0
SHEET 2 D 2 GLN B 242 TYR B 243 -1 O TYR B 243 N GLY B 235
SITE 1 AC1 2 GLY A 39 GLU A 43
SITE 1 AC2 19 SER A 68 ASP A 70 LYS A 92 HIS A 94
SITE 2 AC2 19 ASP A 123 ILE A 179 MET A 182 SER A 183
SITE 3 AC2 19 ILE A 212 PRO A 228 GLN A 241 TYR A 243
SITE 4 AC2 19 GLY A 261 ARG A 262 HOH A3002 HOH A3006
SITE 5 AC2 19 HOH A3074 ASP B 128 THR B 132
SITE 1 AC3 20 ASP A 128 ILE A 129 THR A 132 SER B 68
SITE 2 AC3 20 ASP B 70 LYS B 92 HIS B 94 ASP B 123
SITE 3 AC3 20 ILE B 179 MET B 182 SER B 183 ILE B 212
SITE 4 AC3 20 PRO B 228 GLN B 241 TYR B 243 GLY B 261
SITE 5 AC3 20 ARG B 262 HOH B1002 HOH B1005 HOH B1015
SITE 1 AC4 6 LYS A 53 ALA A 113 GLU A 117 PHE A 118
SITE 2 AC4 6 ASP A 149 HOH A3099
SITE 1 AC5 5 ARG A 46 HIS A 48 PRO A 49 SER A 205
SITE 2 AC5 5 HOH A3117
CRYST1 69.552 61.554 70.989 90.00 111.81 90.00 P 1 21 1 4
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 0.014378 0.000000 0.005752 0.00000
SCALE2 0.000000 0.016246 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015172 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
