HEADER LYASE 15-JUN-07 2QAF
TITLE CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM OROTIDINE 5'-PHOSPHATE
TITLE 2 DECARBOXYLASE COVALENTLY MODIFIED BY 6-IODO-UMP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: OROTIDINE 5' MONOPHOSPHATE DECARBOXYLASE;
COMPND 3 CHAIN: A, B;
COMPND 4 EC: 4.1.1.23;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM;
SOURCE 3 ORGANISM_TAXID: 36329;
SOURCE 4 STRAIN: 3D7;
SOURCE 5 GENE: OMPDC;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-RIL(DE23);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A-LIC
KEYWDS PLASMODIUM FALCIPARUM, OROTIDINE 5'-PHOSPHATE DECARBOXYLASE,
KEYWDS 2 COVALENTLY, 6-IODO-UMP, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.LIU,W.LAU,A.M.BELLO,L.P.KOTRA,R.HUI,E.F.PAI
REVDAT 5 30-AUG-23 2QAF 1 REMARK SEQADV LINK
REVDAT 4 24-JAN-18 2QAF 1 AUTHOR
REVDAT 3 13-JUL-11 2QAF 1 VERSN
REVDAT 2 24-FEB-09 2QAF 1 VERSN
REVDAT 1 29-APR-08 2QAF 0
JRNL AUTH A.M.BELLO,E.PODUCH,Y.LIU,L.WEI,I.CRANDALL,X.WANG,C.DYANAND,
JRNL AUTH 2 K.C.KAIN,E.F.PAI,L.P.KOTRA
JRNL TITL STRUCTURE-ACTIVITY RELATIONSHIPS OF C6-URIDINE DERIVATIVES
JRNL TITL 2 TARGETING PLASMODIA OROTIDINE MONOPHOSPHATE DECARBOXYLASE
JRNL REF J.MED.CHEM. V. 51 439 2008
JRNL REFN ISSN 0022-2623
JRNL PMID 18189347
JRNL DOI 10.1021/JM7010673
REMARK 2
REMARK 2 RESOLUTION. 1.95 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) : 1.95
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.30
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4
REMARK 3 NUMBER OF REFLECTIONS : 41065
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) : 0.175
REMARK 3 R VALUE (WORKING SET) : 0.172
REMARK 3 FREE R VALUE : 0.226
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2191
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) : 1.95
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2955
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.34
REMARK 3 BIN R VALUE (WORKING SET) : 0.1870
REMARK 3 BIN FREE R VALUE SET COUNT : 152
REMARK 3 BIN FREE R VALUE : 0.2480
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5354
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 47
REMARK 3 SOLVENT ATOMS : 250
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.81
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.55000
REMARK 3 B22 (A**2) : 0.28000
REMARK 3 B33 (A**2) : -0.83000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.194
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.170
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.455
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5589 ; 0.010 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7549 ; 1.633 ; 1.968
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 661 ; 6.198 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 288 ;40.403 ;25.764
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1018 ;14.800 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;24.152 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 804 ; 0.120 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4241 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2697 ; 0.232 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3941 ; 0.315 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 313 ; 0.158 ; 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): 74 ; 0.188 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.213 ; 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): 3386 ; 1.152 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5337 ; 1.730 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2536 ; 2.885 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2212 ; 4.188 ; 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 2QAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-07.
REMARK 100 THE DEPOSITION ID IS D_1000043351.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-FEB-07
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 14-BM-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.90020
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41322
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950
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 (%) : 95.4
REMARK 200 DATA REDUNDANCY : 4.700
REMARK 200 R MERGE (I) : 0.10200
REMARK 200 R SYM (I) : 0.10200
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0
REMARK 200 DATA REDUNDANCY IN SHELL : 4.30
REMARK 200 R MERGE FOR SHELL (I) : 0.49200
REMARK 200 R SYM FOR SHELL (I) : 0.49200
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300
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: PDB ENTRY 2Q8L
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 35.60
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 1000, 100MM AMMONIUM
REMARK 280 PHOSPHATE, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z
REMARK 290 4555 X+1/2,-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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 40.46000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.92450
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.46000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.92450
REMARK 290 SMTRY3 4 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: 6360 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 24410 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.8 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 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 A3046 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A3073 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 -18
REMARK 465 GLY A -17
REMARK 465 SER A -16
REMARK 465 SER A -15
REMARK 465 HIS A -14
REMARK 465 HIS A -13
REMARK 465 HIS A -12
REMARK 465 HIS A -11
REMARK 465 HIS A -10
REMARK 465 HIS A -9
REMARK 465 SER A -8
REMARK 465 SER A -7
REMARK 465 SER A 323
REMARK 465 MET B -18
REMARK 465 GLY B -17
REMARK 465 SER B -16
REMARK 465 SER B -15
REMARK 465 HIS B -14
REMARK 465 HIS B -13
REMARK 465 HIS B -12
REMARK 465 HIS B -11
REMARK 465 HIS B -10
REMARK 465 HIS B -9
REMARK 465 SER B -8
REMARK 465 SER B -7
REMARK 465 GLY B -6
REMARK 465 LEU B -5
REMARK 465 VAL B -4
REMARK 465 PRO B -3
REMARK 465 ARG B -2
REMARK 465 GLY B -1
REMARK 465 GLU B 322
REMARK 465 SER B 323
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 0 49.99 -104.66
REMARK 500 MET A 137 -8.25 -140.21
REMARK 500 ASP A 141 -179.01 -179.27
REMARK 500 VAL A 192 -60.20 -120.45
REMARK 500 ASP A 209 -124.41 57.03
REMARK 500 SER A 245 73.29 -101.63
REMARK 500 VAL B 192 -62.36 -121.69
REMARK 500 ASP B 209 -125.54 55.99
REMARK 500 SER B 245 70.17 -107.60
REMARK 500 ASN B 270 -1.57 77.32
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 THE AUTHORS STATE THAT THERE IS A COVALENT BOND FORMED
REMARK 600 BETWEEN CARBON-6 OF THE URIDINE RING OF UMP AND THE
REMARK 600 NZ-NITROGEN OF LYS138
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1000
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P A 3000
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P B 3000
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2Q8L RELATED DB: PDB
REMARK 900 APO STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM P.
REMARK 900 FALCIPARUM
REMARK 900 RELATED ID: 2Q8Z RELATED DB: PDB
REMARK 900 STRUCTURE OF P. FALCIPARUM OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
REMARK 900 COMPLEXED WITH 6-AMINO-UMP
DBREF 2QAF A 1 323 UNP Q8T6J6 Q8T6J6_PLAFA 1 323
DBREF 2QAF B 1 323 UNP Q8T6J6 Q8T6J6_PLAFA 1 323
SEQADV 2QAF MET A -18 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF GLY A -17 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF SER A -16 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF SER A -15 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS A -14 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS A -13 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS A -12 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS A -11 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS A -10 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS A -9 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF SER A -8 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF SER A -7 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF GLY A -6 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF LEU A -5 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF VAL A -4 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF PRO A -3 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF ARG A -2 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF GLY A -1 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF SER A 0 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF MET B -18 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF GLY B -17 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF SER B -16 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF SER B -15 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS B -14 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS B -13 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS B -12 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS B -11 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS B -10 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF HIS B -9 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF SER B -8 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF SER B -7 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF GLY B -6 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF LEU B -5 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF VAL B -4 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF PRO B -3 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF ARG B -2 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF GLY B -1 UNP Q8T6J6 EXPRESSION TAG
SEQADV 2QAF SER B 0 UNP Q8T6J6 EXPRESSION TAG
SEQRES 1 A 342 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES 2 A 342 LEU VAL PRO ARG GLY SER MET GLY PHE LYS VAL LYS LEU
SEQRES 3 A 342 GLU LYS ARG ARG ASN ALA ILE ASN THR CYS LEU CYS ILE
SEQRES 4 A 342 GLY LEU ASP PRO ASP GLU LYS ASP ILE GLU ASN PHE MET
SEQRES 5 A 342 LYS ASN GLU LYS GLU ASN ASN TYR ASN ASN ILE LYS LYS
SEQRES 6 A 342 ASN LEU LYS GLU LYS TYR ILE ASN ASN VAL SER ILE LYS
SEQRES 7 A 342 LYS ASP ILE LEU LEU LYS ALA PRO ASP ASN ILE ILE ARG
SEQRES 8 A 342 GLU GLU LYS SER GLU GLU PHE PHE TYR PHE PHE ASN HIS
SEQRES 9 A 342 PHE CYS PHE TYR ILE ILE ASN GLU THR ASN LYS TYR ALA
SEQRES 10 A 342 LEU THR PHE LYS MET ASN PHE ALA PHE TYR ILE PRO TYR
SEQRES 11 A 342 GLY SER VAL GLY ILE ASP VAL LEU LYS ASN VAL PHE ASP
SEQRES 12 A 342 TYR LEU TYR GLU LEU ASN ILE PRO THR ILE LEU ASP MET
SEQRES 13 A 342 LYS ILE ASN ASP ILE GLY ASN THR VAL LYS ASN TYR ARG
SEQRES 14 A 342 LYS PHE ILE PHE GLU TYR LEU LYS SER ASP SER CYS THR
SEQRES 15 A 342 VAL ASN ILE TYR MET GLY THR ASN MET LEU LYS ASP ILE
SEQRES 16 A 342 CYS TYR ASP GLU GLU LYS ASN LYS TYR TYR SER ALA PHE
SEQRES 17 A 342 VAL LEU VAL LYS THR THR ASN PRO ASP SER ALA ILE PHE
SEQRES 18 A 342 GLN LYS ASN LEU SER LEU ASP ASN LYS GLN ALA TYR VAL
SEQRES 19 A 342 ILE MET ALA GLN GLU ALA LEU ASN MET SER SER TYR LEU
SEQRES 20 A 342 ASN LEU GLU GLN ASN ASN GLU PHE ILE GLY PHE VAL VAL
SEQRES 21 A 342 GLY ALA ASN SER TYR ASP GLU MET ASN TYR ILE ARG THR
SEQRES 22 A 342 TYR PHE PRO ASN CYS TYR ILE LEU SER PRO GLY ILE GLY
SEQRES 23 A 342 ALA GLN ASN GLY ASP LEU HIS LYS THR LEU THR ASN GLY
SEQRES 24 A 342 TYR HIS LYS SER TYR GLU LYS ILE LEU ILE ASN ILE GLY
SEQRES 25 A 342 ARG ALA ILE THR LYS ASN PRO TYR PRO GLN LYS ALA ALA
SEQRES 26 A 342 GLN MET TYR TYR ASP GLN ILE ASN ALA ILE LEU LYS GLN
SEQRES 27 A 342 ASN MET GLU SER
SEQRES 1 B 342 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES 2 B 342 LEU VAL PRO ARG GLY SER MET GLY PHE LYS VAL LYS LEU
SEQRES 3 B 342 GLU LYS ARG ARG ASN ALA ILE ASN THR CYS LEU CYS ILE
SEQRES 4 B 342 GLY LEU ASP PRO ASP GLU LYS ASP ILE GLU ASN PHE MET
SEQRES 5 B 342 LYS ASN GLU LYS GLU ASN ASN TYR ASN ASN ILE LYS LYS
SEQRES 6 B 342 ASN LEU LYS GLU LYS TYR ILE ASN ASN VAL SER ILE LYS
SEQRES 7 B 342 LYS ASP ILE LEU LEU LYS ALA PRO ASP ASN ILE ILE ARG
SEQRES 8 B 342 GLU GLU LYS SER GLU GLU PHE PHE TYR PHE PHE ASN HIS
SEQRES 9 B 342 PHE CYS PHE TYR ILE ILE ASN GLU THR ASN LYS TYR ALA
SEQRES 10 B 342 LEU THR PHE LYS MET ASN PHE ALA PHE TYR ILE PRO TYR
SEQRES 11 B 342 GLY SER VAL GLY ILE ASP VAL LEU LYS ASN VAL PHE ASP
SEQRES 12 B 342 TYR LEU TYR GLU LEU ASN ILE PRO THR ILE LEU ASP MET
SEQRES 13 B 342 LYS ILE ASN ASP ILE GLY ASN THR VAL LYS ASN TYR ARG
SEQRES 14 B 342 LYS PHE ILE PHE GLU TYR LEU LYS SER ASP SER CYS THR
SEQRES 15 B 342 VAL ASN ILE TYR MET GLY THR ASN MET LEU LYS ASP ILE
SEQRES 16 B 342 CYS TYR ASP GLU GLU LYS ASN LYS TYR TYR SER ALA PHE
SEQRES 17 B 342 VAL LEU VAL LYS THR THR ASN PRO ASP SER ALA ILE PHE
SEQRES 18 B 342 GLN LYS ASN LEU SER LEU ASP ASN LYS GLN ALA TYR VAL
SEQRES 19 B 342 ILE MET ALA GLN GLU ALA LEU ASN MET SER SER TYR LEU
SEQRES 20 B 342 ASN LEU GLU GLN ASN ASN GLU PHE ILE GLY PHE VAL VAL
SEQRES 21 B 342 GLY ALA ASN SER TYR ASP GLU MET ASN TYR ILE ARG THR
SEQRES 22 B 342 TYR PHE PRO ASN CYS TYR ILE LEU SER PRO GLY ILE GLY
SEQRES 23 B 342 ALA GLN ASN GLY ASP LEU HIS LYS THR LEU THR ASN GLY
SEQRES 24 B 342 TYR HIS LYS SER TYR GLU LYS ILE LEU ILE ASN ILE GLY
SEQRES 25 B 342 ARG ALA ILE THR LYS ASN PRO TYR PRO GLN LYS ALA ALA
SEQRES 26 B 342 GLN MET TYR TYR ASP GLN ILE ASN ALA ILE LEU LYS GLN
SEQRES 27 B 342 ASN MET GLU SER
HET U5P A3000 21
HET SO4 B1000 5
HET U5P B3000 21
HETNAM U5P URIDINE-5'-MONOPHOSPHATE
HETNAM SO4 SULFATE ION
FORMUL 3 U5P 2(C9 H13 N2 O9 P)
FORMUL 4 SO4 O4 S 2-
FORMUL 6 HOH *250(H2 O)
HELIX 1 1 GLY A 2 ASN A 15 1 14
HELIX 2 2 ASP A 25 ASN A 39 1 15
HELIX 3 3 TYR A 41 GLU A 50 1 10
HELIX 4 4 LYS A 51 VAL A 56 5 6
HELIX 5 5 LYS A 59 LEU A 64 1 6
HELIX 6 6 ALA A 66 GLU A 74 1 9
HELIX 7 7 GLU A 77 ASN A 95 1 19
HELIX 8 8 LYS A 96 ALA A 98 5 3
HELIX 9 9 ALA A 106 TYR A 108 5 3
HELIX 10 10 GLY A 112 ASN A 130 1 19
HELIX 11 11 ILE A 142 GLU A 155 1 14
HELIX 12 12 ASN A 165 ILE A 176 5 12
HELIX 13 13 SER A 199 LYS A 204 1 6
HELIX 14 14 ALA A 213 ASN A 229 1 17
HELIX 15 15 LEU A 230 ASN A 234 5 5
HELIX 16 16 SER A 245 PHE A 256 1 12
HELIX 17 17 ASP A 272 TYR A 281 1 10
HELIX 18 18 SER A 284 GLU A 286 5 3
HELIX 19 19 GLY A 293 LYS A 298 1 6
HELIX 20 20 TYR A 301 GLU A 322 1 22
HELIX 21 21 GLY B 2 ASN B 15 1 14
HELIX 22 22 ASP B 25 ASN B 39 1 15
HELIX 23 23 TYR B 41 LEU B 48 1 8
HELIX 24 24 LYS B 49 VAL B 56 5 8
HELIX 25 25 LYS B 59 LEU B 64 1 6
HELIX 26 26 ALA B 66 GLU B 74 1 9
HELIX 27 27 GLU B 77 ASN B 95 1 19
HELIX 28 28 LYS B 96 ALA B 98 5 3
HELIX 29 29 ALA B 106 TYR B 108 5 3
HELIX 30 30 GLY B 112 LEU B 129 1 18
HELIX 31 31 ILE B 142 GLU B 155 1 14
HELIX 32 32 THR B 170 ILE B 176 5 7
HELIX 33 33 SER B 199 LYS B 204 1 6
HELIX 34 34 ALA B 213 ASN B 229 1 17
HELIX 35 35 LEU B 230 ASN B 234 5 5
HELIX 36 36 SER B 245 PHE B 256 1 12
HELIX 37 37 ASP B 272 TYR B 281 1 10
HELIX 38 38 SER B 284 GLU B 286 5 3
HELIX 39 39 GLY B 293 LYS B 298 1 6
HELIX 40 40 TYR B 301 MET B 321 1 21
SHEET 1 A 9 LEU A 18 LEU A 22 0
SHEET 2 A 9 THR A 100 ASN A 104 1 O LYS A 102 N LEU A 22
SHEET 3 A 9 THR A 133 ASP A 136 1 O ASP A 136 N MET A 103
SHEET 4 A 9 SER A 161 VAL A 164 1 O SER A 161 N LEU A 135
SHEET 5 A 9 SER A 187 LYS A 193 1 O PHE A 189 N CYS A 162
SHEET 6 A 9 ILE A 237 VAL A 241 1 O GLY A 238 N VAL A 190
SHEET 7 A 9 ILE A 261 SER A 263 1 O LEU A 262 N PHE A 239
SHEET 8 A 9 ILE A 288 ILE A 292 1 O LEU A 289 N SER A 263
SHEET 9 A 9 LEU A 18 LEU A 22 1 N CYS A 19 O ILE A 290
SHEET 1 B 2 TYR A 178 ASP A 179 0
SHEET 2 B 2 LYS A 184 TYR A 185 -1 O LYS A 184 N ASP A 179
SHEET 1 C 2 SER A 207 LEU A 208 0
SHEET 2 C 2 LYS A 211 GLN A 212 -1 O LYS A 211 N LEU A 208
SHEET 1 D 9 LEU B 18 LEU B 22 0
SHEET 2 D 9 THR B 100 ASN B 104 1 O LYS B 102 N LEU B 22
SHEET 3 D 9 THR B 133 ILE B 139 1 O ASP B 136 N MET B 103
SHEET 4 D 9 SER B 161 VAL B 164 1 O SER B 161 N LEU B 135
SHEET 5 D 9 SER B 187 LYS B 193 1 O PHE B 189 N CYS B 162
SHEET 6 D 9 ILE B 237 VAL B 241 1 O VAL B 240 N VAL B 190
SHEET 7 D 9 ILE B 261 SER B 263 1 O LEU B 262 N PHE B 239
SHEET 8 D 9 ILE B 288 ILE B 292 1 O LEU B 289 N SER B 263
SHEET 9 D 9 LEU B 18 LEU B 22 1 N CYS B 19 O ILE B 290
SHEET 1 E 2 TYR B 178 ASP B 179 0
SHEET 2 E 2 LYS B 184 TYR B 185 -1 O LYS B 184 N ASP B 179
SHEET 1 F 2 SER B 207 LEU B 208 0
SHEET 2 F 2 LYS B 211 GLN B 212 -1 O LYS B 211 N LEU B 208
LINK NZ LYS A 138 C6 U5P A3000 1555 1555 1.36
LINK NZ LYS B 138 C6 U5P B3000 1555 1555 1.36
SITE 1 AC1 5 LYS B 147 ARG B 150 ASP B 179 GLU B 180
SITE 2 AC1 5 GLU B 181
SITE 1 AC2 19 ASP A 23 LYS A 102 ASN A 104 ASP A 136
SITE 2 AC2 19 LYS A 138 THR A 194 THR A 195 PRO A 264
SITE 3 AC2 19 GLN A 269 GLY A 293 ARG A 294 HOH A3002
SITE 4 AC2 19 HOH A3003 HOH A3008 HOH A3010 HOH A3019
SITE 5 AC2 19 ASP B 141 ILE B 142 THR B 145
SITE 1 AC3 19 ASP A 141 ILE A 142 THR A 145 ASP B 23
SITE 2 AC3 19 LYS B 102 ASN B 104 ASP B 136 LYS B 138
SITE 3 AC3 19 THR B 194 THR B 195 PRO B 264 GLN B 269
SITE 4 AC3 19 GLY B 293 ARG B 294 HOH B3004 HOH B3007
SITE 5 AC3 19 HOH B3014 HOH B3015 HOH B3016
CRYST1 80.920 83.849 89.869 90.00 90.00 90.00 P 21 21 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 0.012358 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011926 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011127 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
