HEADER LYASE 19-JUN-07 2QCF
TITLE CRYSTAL STRUCTURE OF THE OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE
TITLE 2 DOMAIN (ASP312ASN MUTANT) OF HUMAN UMP SYNTHASE BOUND TO 5-FLUORO-UMP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: URIDINE 5'-MONOPHOSPHATE SYNTHASE (UMP SYNTHASE);
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: C-TERMINAL DOMAIN;
COMPND 5 EC: 4.1.1.23;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: 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 ROSETTA 2(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM-30
KEYWDS UMP SYNTHASE, DECARBOXYLASE, CATALYTIC PROFICIENCY, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.WITTMANN,M.RUDOLPH
REVDAT 6 20-OCT-21 2QCF 1 REMARK SEQADV LINK
REVDAT 5 13-JUL-11 2QCF 1 VERSN
REVDAT 4 24-FEB-09 2QCF 1 VERSN
REVDAT 3 18-MAR-08 2QCF 1 REMARK
REVDAT 2 12-FEB-08 2QCF 1 JRNL
REVDAT 1 06-NOV-07 2QCF 0
JRNL AUTH J.G.WITTMANN,D.HEINRICH,K.GASOW,A.FREY,U.DIEDERICHSEN,
JRNL AUTH 2 M.G.RUDOLPH
JRNL TITL STRUCTURES OF THE HUMAN OROTIDINE-5'-MONOPHOSPHATE
JRNL TITL 2 DECARBOXYLASE SUPPORT A COVALENT MECHANISM AND PROVIDE A
JRNL TITL 3 FRAMEWORK FOR DRUG DESIGN.
JRNL REF STRUCTURE V. 16 82 2008
JRNL REFN ISSN 0969-2126
JRNL PMID 18184586
JRNL DOI 10.1016/J.STR.2007.10.020
REMARK 2
REMARK 2 RESOLUTION. 1.22 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) : 1.22
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.14
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 77246
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) : 0.123
REMARK 3 R VALUE (WORKING SET) : 0.121
REMARK 3 FREE R VALUE : 0.148
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 4111
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) : 1.22
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.25
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5410
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.25
REMARK 3 BIN R VALUE (WORKING SET) : 0.2610
REMARK 3 BIN FREE R VALUE SET COUNT : 310
REMARK 3 BIN FREE R VALUE : 0.2820
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1967
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 28
REMARK 3 SOLVENT ATOMS : 382
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.11
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.95000
REMARK 3 B22 (A**2) : -0.44000
REMARK 3 B33 (A**2) : -0.52000
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): 0.033
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.034
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.171
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.977
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2344 ; 0.019 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 1659 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3230 ; 1.840 ; 1.998
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4124 ; 1.047 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 345 ; 6.229 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;35.141 ;24.020
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 469 ;13.118 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;16.047 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 373 ; 0.125 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2667 ; 0.009 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 465 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 537 ; 0.254 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2070 ; 0.215 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1193 ; 0.198 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 1510 ; 0.094 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 343 ; 0.211 ; 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): 28 ; 0.282 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 58 ; 0.331 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 54 ; 0.317 ; 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): 1796 ; 1.924 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 581 ; 0.672 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2338 ; 2.090 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1016 ; 3.472 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 849 ; 4.666 ; 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): 4714 ; 1.735 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 383 ; 9.432 ; 3.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3924 ; 2.920 ; 3.000
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 : BABINET MODEL WITH MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ATOMS THAT
REMARK 3 ARE
REMARK 3 IN CLOSE CONTACT HAVE OCCUPANCY LESS THAN 1 AND ARE MUTUALLY
REMARK 3 EXCLUSIVE.
REMARK 4
REMARK 4 2QCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-07.
REMARK 100 THE DEPOSITION ID IS D_1000043423.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-MAR-06
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG
REMARK 200 BEAMLINE : X13
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.8
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81404
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220
REMARK 200 RESOLUTION RANGE LOW (A) : 22.140
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 6.400
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.08300
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.22
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : 4.60
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.59400
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.85
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
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
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 30.68500
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 30.68500
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 38.40750
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.75600
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.40750
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.75600
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.68500
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.40750
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.75600
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.68500
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.40750
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.75600
REMARK 290 SMTRY3 8 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: 5430 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 18050 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 0.00000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 61.37000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 560 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 GLY A 221
REMARK 465 ALA A 222
REMARK 465 VAL A 480
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O HOH A 709 O HOH A 825 1.60
REMARK 500 O HOH A 710 O HOH A 793 1.98
REMARK 500 O HOH A 699 O HOH A 830 2.03
REMARK 500 OG SER A 476 O HOH A 727 2.03
REMARK 500 O HOH A 855 O HOH A 868 2.08
REMARK 500 O HOH A 796 O HOH A 815 2.10
REMARK 500 O HOH A 680 O HOH A 793 2.11
REMARK 500 O HOH A 763 O HOH A 838 2.11
REMARK 500 CD1 ILE A 454 O HOH A 796 2.13
REMARK 500 O HOH A 687 O HOH A 764 2.16
REMARK 500 O HOH A 655 O HOH A 757 2.18
REMARK 500 O HOH A 631 O HOH A 783 2.18
REMARK 500 OE1 GLU A 461 O HOH A 823 2.19
REMARK 500 O HOH A 783 O HOH A 832 2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 764 O HOH A 844 3555 2.10
REMARK 500 O HOH A 814 O HOH A 819 6554 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 245 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 ARG A 245 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 ASP A 317 CB - CG - OD1 ANGL. DEV. = 12.0 DEGREES
REMARK 500 ARG A 477 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES
REMARK 500 ARG A 477 NE - CZ - NH2 ANGL. DEV. = 6.5 DEGREES
REMARK 500 LEU A 478 CA - CB - CG ANGL. DEV. = 14.5 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 GLU A 306 76.21 67.28
REMARK 500 ALA A 316 36.48 -161.69
REMARK 500 ALA A 316 42.87 -161.69
REMARK 500 LYS A 332 59.14 39.36
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 5FU A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 502
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2QCC RELATED DB: PDB
REMARK 900 RELATED ID: 2QCD RELATED DB: PDB
REMARK 900 RELATED ID: 2QCE RELATED DB: PDB
REMARK 900 RELATED ID: 2V30 RELATED DB: PDB
REMARK 900 RELATED ID: 2JGY RELATED DB: PDB
DBREF 2QCF A 224 480 UNP P11172 PYR5_HUMAN 224 480
SEQADV 2QCF GLY A 221 UNP P11172 EXPRESSION TAG
SEQADV 2QCF ALA A 222 UNP P11172 EXPRESSION TAG
SEQADV 2QCF MET A 223 UNP P11172 EXPRESSION TAG
SEQADV 2QCF ASN A 312 UNP P11172 ASP 312 ENGINEERED MUTATION
SEQRES 1 A 260 GLY ALA MET GLU LEU SER PHE GLY ALA ARG ALA GLU LEU
SEQRES 2 A 260 PRO ARG ILE HIS PRO VAL ALA SER LYS LEU LEU ARG LEU
SEQRES 3 A 260 MET GLN LYS LYS GLU THR ASN LEU CYS LEU SER ALA ASP
SEQRES 4 A 260 VAL SER LEU ALA ARG GLU LEU LEU GLN LEU ALA ASP ALA
SEQRES 5 A 260 LEU GLY PRO SER ILE CYS MET LEU LYS THR HIS VAL ASP
SEQRES 6 A 260 ILE LEU ASN ASP PHE THR LEU ASP VAL MET LYS GLU LEU
SEQRES 7 A 260 ILE THR LEU ALA LYS CSS HIS GLU PHE LEU ILE PHE GLU
SEQRES 8 A 260 ASN ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LYS
SEQRES 9 A 260 GLN TYR GLU GLY GLY ILE PHE LYS ILE ALA SER TRP ALA
SEQRES 10 A 260 ASP LEU VAL ASN ALA HIS VAL VAL PRO GLY SER GLY VAL
SEQRES 11 A 260 VAL LYS GLY LEU GLN GLU VAL GLY LEU PRO LEU HIS ARG
SEQRES 12 A 260 GLY CYS LEU LEU ILE ALA GLU MET SER SER THR GLY SER
SEQRES 13 A 260 LEU ALA THR GLY ASP TYR THR ARG ALA ALA VAL ARG MET
SEQRES 14 A 260 ALA GLU GLU HIS SER GLU PHE VAL VAL GLY PHE ILE SER
SEQRES 15 A 260 GLY SER ARG VAL SER MET LYS PRO GLU PHE LEU HIS LEU
SEQRES 16 A 260 THR PRO GLY VAL GLN LEU GLU ALA GLY GLY ASP ASN LEU
SEQRES 17 A 260 GLY GLN GLN TYR ASN SER PRO GLN GLU VAL ILE GLY LYS
SEQRES 18 A 260 ARG GLY SER ASP ILE ILE ILE VAL GLY ARG GLY ILE ILE
SEQRES 19 A 260 SER ALA ALA ASP ARG LEU GLU ALA ALA GLU MET TYR ARG
SEQRES 20 A 260 LYS ALA ALA TRP GLU ALA TYR LEU SER ARG LEU GLY VAL
MODRES 2QCF CSS A 304 CYS S-MERCAPTOCYSTEINE
HET CSS A 304 7
HET 5FU A 501 22
HET GOL A 502 6
HETNAM CSS S-MERCAPTOCYSTEINE
HETNAM 5FU 5-FLUORO-URIDINE-5'-MONOPHOSPHATE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 1 CSS C3 H7 N O2 S2
FORMUL 2 5FU C9 H12 F N2 O9 P
FORMUL 3 GOL C3 H8 O3
FORMUL 4 HOH *382(H2 O)
HELIX 1 1 SER A 226 ALA A 231 1 6
HELIX 2 2 HIS A 237 GLU A 251 1 15
HELIX 3 3 LEU A 262 GLY A 274 1 13
HELIX 4 4 PRO A 275 ILE A 277 5 3
HELIX 5 5 HIS A 283 LEU A 287 5 5
HELIX 6 6 THR A 291 GLU A 306 1 16
HELIX 7 7 ILE A 318 GLY A 328 1 11
HELIX 8 8 LYS A 332 ALA A 337 1 6
HELIX 9 9 SER A 348 LEU A 359 1 12
HELIX 10 10 THR A 379 GLU A 392 1 14
HELIX 11 11 SER A 434 LYS A 441 1 8
HELIX 12 12 GLY A 450 SER A 455 1 6
HELIX 13 13 ASP A 458 GLY A 479 1 22
SHEET 1 A 9 LEU A 254 SER A 257 0
SHEET 2 A 9 MET A 279 THR A 282 1 O LYS A 281 N LEU A 256
SHEET 3 A 9 LEU A 308 PHE A 315 1 O ASN A 312 N THR A 282
SHEET 4 A 9 LEU A 339 HIS A 343 1 O HIS A 343 N PHE A 315
SHEET 5 A 9 GLY A 364 ILE A 368 1 O ILE A 368 N ALA A 342
SHEET 6 A 9 VAL A 397 ILE A 401 1 O VAL A 398 N CYS A 365
SHEET 7 A 9 LEU A 413 THR A 416 1 O LEU A 413 N PHE A 400
SHEET 8 A 9 ILE A 446 VAL A 449 1 O ILE A 448 N THR A 416
SHEET 9 A 9 LEU A 254 SER A 257 1 N CYS A 255 O ILE A 447
LINK C LYS A 303 N CSS A 304 1555 1555 1.33
LINK C CSS A 304 N HIS A 305 1555 1555 1.32
SITE 1 AC1 20 SER A 257 ASP A 259 LYS A 281 HIS A 283
SITE 2 AC1 20 ASN A 312 LYS A 314 ASP A 317 ILE A 318
SITE 3 AC1 20 THR A 321 MET A 371 SER A 372 ILE A 401
SITE 4 AC1 20 PRO A 417 GLN A 430 TYR A 432 GLY A 450
SITE 5 AC1 20 ARG A 451 HOH A 503 HOH A 505 HOH A 513
SITE 1 AC2 7 GLY A 228 ALA A 229 GLN A 248 LEU A 421
SITE 2 AC2 7 ALA A 423 HOH A 555 HOH A 601
CRYST1 76.815 115.512 61.370 90.00 90.00 90.00 C 2 2 21 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 0.013018 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008657 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016295 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
