HEADER LYASE 05-JAN-00 1DQW TITLE CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 4.1.1.23; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PCDA6022 KEYWDS TIM BARREL, OROTIDINE 5'-PHOSPHATE, URIDINE 5'-PHOSPHATE, KEYWDS 2 DECARBOXYLASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.V.MILBURN,B.G.MILLER,A.M.HASSELL,R.WOLFENDEN,S.A.SHORT REVDAT 5 07-FEB-24 1DQW 1 REMARK REVDAT 4 03-NOV-21 1DQW 1 SEQADV REVDAT 3 04-OCT-17 1DQW 1 REMARK REVDAT 2 24-FEB-09 1DQW 1 VERSN REVDAT 1 20-MAR-00 1DQW 0 JRNL AUTH B.G.MILLER,A.M.HASSELL,R.WOLFENDEN,M.V.MILBURN,S.A.SHORT JRNL TITL ANATOMY OF A PROFICIENT ENZYME: THE STRUCTURE OF OROTIDINE JRNL TITL 2 5'-MONOPHOSPHATE DECARBOXYLASE IN THE PRESENCE AND ABSENCE JRNL TITL 3 OF A POTENTIAL TRANSITION STATE ANALOG. JRNL REF PROC.NATL.ACAD.SCI.USA V. 97 2011 2000 JRNL REFN ISSN 0027-8424 JRNL PMID 10681417 JRNL DOI 10.1073/PNAS.030409797 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2473075.210 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 65044 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) : 0.218 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.200 REMARK 3 FREE R VALUE TEST SET COUNT : 5311 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4889 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 452 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8236 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 874 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.44000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : -3.09000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.180 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.940 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.880 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.800 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 85.65 REMARK 3 REMARK 3 NCS MODEL : CONSTRAINED 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.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DQW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000010308. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0281 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70148 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 97.1 REMARK 200 DATA REDUNDANCY : 15.10 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : 0.11300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM-HEPES, ISOPROPANOL, REMARK 280 POLYETHYLENE GLYCOL 4000, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 278.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 45.03000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.48950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.10850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.48950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.03000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.10850 REMARK 290 SMTRY3 4 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER OF MOLECULE A RELATED BY REMARK 300 A TWO-FOLD SYMMETRY AXIS TO MOLECULE B, OR MOLECULE C RELATED BY A REMARK 300 TWO-FOLD SYMMETRY AXIS TO MOLECULE D. 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: 2930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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: 2940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 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 GLY C 205 N LEU C 206 0.52 REMARK 500 O GLY A 205 N LEU A 206 0.52 REMARK 500 O GLY D 205 N LEU D 206 0.59 REMARK 500 O GLY B 205 N LEU B 206 0.66 REMARK 500 O GLY B 205 CA LEU B 206 1.14 REMARK 500 O GLY D 205 CA LEU D 206 1.16 REMARK 500 O GLY C 205 CA LEU C 206 1.20 REMARK 500 O GLY A 205 CA LEU A 206 1.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 217 C ARG A 218 N -0.170 REMARK 500 TYR B 217 C ARG B 218 N -0.168 REMARK 500 TYR C 217 C ARG C 218 N -0.217 REMARK 500 TYR D 217 C ARG D 218 N -0.158 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 GLY A 205 CA - C - N ANGL. DEV. = -15.9 DEGREES REMARK 500 GLY A 205 O - C - N ANGL. DEV. = 101.7 DEGREES REMARK 500 TYR A 217 CA - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 TYR A 217 O - C - N ANGL. DEV. = -14.7 DEGREES REMARK 500 ARG A 218 C - N - CA ANGL. DEV. = 17.2 DEGREES REMARK 500 GLY B 205 CA - C - N ANGL. DEV. = -20.5 DEGREES REMARK 500 GLY B 205 O - C - N ANGL. DEV. = -96.3 DEGREES REMARK 500 LEU B 206 C - N - CA ANGL. DEV. = -16.6 DEGREES REMARK 500 TYR B 217 CA - C - N ANGL. DEV. = 21.1 DEGREES REMARK 500 TYR B 217 O - C - N ANGL. DEV. = -22.0 DEGREES REMARK 500 ARG B 218 C - N - CA ANGL. DEV. = 25.7 DEGREES REMARK 500 GLY C 205 CA - C - N ANGL. DEV. = -16.9 DEGREES REMARK 500 GLY C 205 O - C - N ANGL. DEV. = 101.6 DEGREES REMARK 500 TYR C 217 CA - C - N ANGL. DEV. = 15.8 DEGREES REMARK 500 TYR C 217 O - C - N ANGL. DEV. = -16.6 DEGREES REMARK 500 ARG C 218 C - N - CA ANGL. DEV. = 20.1 DEGREES REMARK 500 GLY D 205 CA - C - N ANGL. DEV. = -19.7 DEGREES REMARK 500 GLY D 205 O - C - N ANGL. DEV. = -99.1 DEGREES REMARK 500 LEU D 206 C - N - CA ANGL. DEV. = -15.0 DEGREES REMARK 500 TYR D 217 CA - C - N ANGL. DEV. = 17.6 DEGREES REMARK 500 TYR D 217 O - C - N ANGL. DEV. = -17.9 DEGREES REMARK 500 ARG D 218 C - N - CA ANGL. DEV. = 20.7 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 HIS A 2 -163.77 -73.35 REMARK 500 ASN A 85 75.18 60.26 REMARK 500 ALA A 95 57.57 -145.11 REMARK 500 ALA A 107 -137.73 -126.76 REMARK 500 ASP A 175 116.54 -173.82 REMARK 500 ASP A 196 78.86 -119.61 REMARK 500 GLN A 215 52.05 77.14 REMARK 500 TYR A 217 -33.48 -146.32 REMARK 500 PHE A 238 -11.29 -140.95 REMARK 500 LYS A 240 78.69 25.99 REMARK 500 GLN A 266 -27.25 -152.53 REMARK 500 LEU B 36 79.89 -106.90 REMARK 500 ASP B 67 47.77 -142.87 REMARK 500 ASN B 85 72.41 53.27 REMARK 500 ALA B 95 56.38 -144.24 REMARK 500 ALA B 107 -140.47 -132.14 REMARK 500 ASP B 175 118.81 -174.85 REMARK 500 GLN B 215 50.95 78.75 REMARK 500 TYR B 217 -36.74 -149.47 REMARK 500 PHE B 238 -7.12 -140.89 REMARK 500 LYS B 240 76.94 30.56 REMARK 500 GLN B 266 -27.26 -151.63 REMARK 500 HIS C 2 -165.52 -73.31 REMARK 500 ASP C 67 45.51 -143.91 REMARK 500 ASN C 85 74.50 61.70 REMARK 500 ALA C 95 56.94 -147.46 REMARK 500 ALA C 107 -136.09 -124.08 REMARK 500 ASP C 175 119.59 -172.48 REMARK 500 GLN C 215 51.12 76.84 REMARK 500 TYR C 217 -27.70 -144.21 REMARK 500 PHE C 238 -8.95 -142.75 REMARK 500 LYS C 240 73.21 32.32 REMARK 500 GLN C 266 -22.41 -154.11 REMARK 500 ASP D 67 49.11 -142.06 REMARK 500 ASN D 85 72.92 58.16 REMARK 500 ALA D 95 55.33 -144.32 REMARK 500 ALA D 107 -136.63 -131.61 REMARK 500 ASP D 175 115.79 -177.01 REMARK 500 ASP D 196 79.59 -119.63 REMARK 500 GLN D 215 55.83 74.37 REMARK 500 TYR D 217 -29.42 -145.89 REMARK 500 PHE D 238 -6.87 -143.21 REMARK 500 LYS D 240 74.85 26.84 REMARK 500 GLN D 266 -27.16 -154.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 205 -16.48 REMARK 500 GLY B 205 -16.81 REMARK 500 GLY C 205 -12.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DQX RELATED DB: PDB REMARK 900 1DQX IS THE CRYSTAL STRUCTURE OF THE SAME PROTEIN COMPLEXED WITH 6- REMARK 900 HYDROXYURIDINE 5'PHOSPHATE. DBREF 1DQW A 1 267 UNP P03962 PYRF_YEAST 1 267 DBREF 1DQW B 1 267 UNP P03962 PYRF_YEAST 1 267 DBREF 1DQW C 1 267 UNP P03962 PYRF_YEAST 1 267 DBREF 1DQW D 1 267 UNP P03962 PYRF_YEAST 1 267 SEQADV 1DQW HIS A 2 UNP P03962 SER 2 ENGINEERED MUTATION SEQADV 1DQW ASP A 267 UNP P03962 ASN 267 ENGINEERED MUTATION SEQADV 1DQW HIS B 2 UNP P03962 SER 2 ENGINEERED MUTATION SEQADV 1DQW ASP B 267 UNP P03962 ASN 267 ENGINEERED MUTATION SEQADV 1DQW HIS C 2 UNP P03962 SER 2 ENGINEERED MUTATION SEQADV 1DQW ASP C 267 UNP P03962 ASN 267 ENGINEERED MUTATION SEQADV 1DQW HIS D 2 UNP P03962 SER 2 ENGINEERED MUTATION SEQADV 1DQW ASP D 267 UNP P03962 ASN 267 ENGINEERED MUTATION SEQRES 1 A 267 MET HIS LYS ALA THR TYR LYS GLU ARG ALA ALA THR HIS SEQRES 2 A 267 PRO SER PRO VAL ALA ALA LYS LEU PHE ASN ILE MET HIS SEQRES 3 A 267 GLU LYS GLN THR ASN LEU CYS ALA SER LEU ASP VAL ARG SEQRES 4 A 267 THR THR LYS GLU LEU LEU GLU LEU VAL GLU ALA LEU GLY SEQRES 5 A 267 PRO LYS ILE CYS LEU LEU LYS THR HIS VAL ASP ILE LEU SEQRES 6 A 267 THR ASP PHE SER MET GLU GLY THR VAL LYS PRO LEU LYS SEQRES 7 A 267 ALA LEU SER ALA LYS TYR ASN PHE LEU LEU PHE GLU ASP SEQRES 8 A 267 ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LEU GLN SEQRES 9 A 267 TYR SER ALA GLY VAL TYR ARG ILE ALA GLU TRP ALA ASP SEQRES 10 A 267 ILE THR ASN ALA HIS GLY VAL VAL GLY PRO GLY ILE VAL SEQRES 11 A 267 SER GLY LEU LYS GLN ALA ALA GLU GLU VAL THR LYS GLU SEQRES 12 A 267 PRO ARG GLY LEU LEU MET LEU ALA GLU LEU SER CYS LYS SEQRES 13 A 267 GLY SER LEU SER THR GLY GLU TYR THR LYS GLY THR VAL SEQRES 14 A 267 ASP ILE ALA LYS SER ASP LYS ASP PHE VAL ILE GLY PHE SEQRES 15 A 267 ILE ALA GLN ARG ASP MET GLY GLY ARG ASP GLU GLY TYR SEQRES 16 A 267 ASP TRP LEU ILE MET THR PRO GLY VAL GLY LEU ASP ASP SEQRES 17 A 267 LYS GLY ASP ALA LEU GLY GLN GLN TYR ARG THR VAL ASP SEQRES 18 A 267 ASP VAL VAL SER THR GLY SER ASP ILE ILE ILE VAL GLY SEQRES 19 A 267 ARG GLY LEU PHE ALA LYS GLY ARG ASP ALA LYS VAL GLU SEQRES 20 A 267 GLY GLU ARG TYR ARG LYS ALA GLY TRP GLU ALA TYR LEU SEQRES 21 A 267 ARG ARG CYS GLY GLN GLN ASP SEQRES 1 B 267 MET HIS LYS ALA THR TYR LYS GLU ARG ALA ALA THR HIS SEQRES 2 B 267 PRO SER PRO VAL ALA ALA LYS LEU PHE ASN ILE MET HIS SEQRES 3 B 267 GLU LYS GLN THR ASN LEU CYS ALA SER LEU ASP VAL ARG SEQRES 4 B 267 THR THR LYS GLU LEU LEU GLU LEU VAL GLU ALA LEU GLY SEQRES 5 B 267 PRO LYS ILE CYS LEU LEU LYS THR HIS VAL ASP ILE LEU SEQRES 6 B 267 THR ASP PHE SER MET GLU GLY THR VAL LYS PRO LEU LYS SEQRES 7 B 267 ALA LEU SER ALA LYS TYR ASN PHE LEU LEU PHE GLU ASP SEQRES 8 B 267 ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LEU GLN SEQRES 9 B 267 TYR SER ALA GLY VAL TYR ARG ILE ALA GLU TRP ALA ASP SEQRES 10 B 267 ILE THR ASN ALA HIS GLY VAL VAL GLY PRO GLY ILE VAL SEQRES 11 B 267 SER GLY LEU LYS GLN ALA ALA GLU GLU VAL THR LYS GLU SEQRES 12 B 267 PRO ARG GLY LEU LEU MET LEU ALA GLU LEU SER CYS LYS SEQRES 13 B 267 GLY SER LEU SER THR GLY GLU TYR THR LYS GLY THR VAL SEQRES 14 B 267 ASP ILE ALA LYS SER ASP LYS ASP PHE VAL ILE GLY PHE SEQRES 15 B 267 ILE ALA GLN ARG ASP MET GLY GLY ARG ASP GLU GLY TYR SEQRES 16 B 267 ASP TRP LEU ILE MET THR PRO GLY VAL GLY LEU ASP ASP SEQRES 17 B 267 LYS GLY ASP ALA LEU GLY GLN GLN TYR ARG THR VAL ASP SEQRES 18 B 267 ASP VAL VAL SER THR GLY SER ASP ILE ILE ILE VAL GLY SEQRES 19 B 267 ARG GLY LEU PHE ALA LYS GLY ARG ASP ALA LYS VAL GLU SEQRES 20 B 267 GLY GLU ARG TYR ARG LYS ALA GLY TRP GLU ALA TYR LEU SEQRES 21 B 267 ARG ARG CYS GLY GLN GLN ASP SEQRES 1 C 267 MET HIS LYS ALA THR TYR LYS GLU ARG ALA ALA THR HIS SEQRES 2 C 267 PRO SER PRO VAL ALA ALA LYS LEU PHE ASN ILE MET HIS SEQRES 3 C 267 GLU LYS GLN THR ASN LEU CYS ALA SER LEU ASP VAL ARG SEQRES 4 C 267 THR THR LYS GLU LEU LEU GLU LEU VAL GLU ALA LEU GLY SEQRES 5 C 267 PRO LYS ILE CYS LEU LEU LYS THR HIS VAL ASP ILE LEU SEQRES 6 C 267 THR ASP PHE SER MET GLU GLY THR VAL LYS PRO LEU LYS SEQRES 7 C 267 ALA LEU SER ALA LYS TYR ASN PHE LEU LEU PHE GLU ASP SEQRES 8 C 267 ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LEU GLN SEQRES 9 C 267 TYR SER ALA GLY VAL TYR ARG ILE ALA GLU TRP ALA ASP SEQRES 10 C 267 ILE THR ASN ALA HIS GLY VAL VAL GLY PRO GLY ILE VAL SEQRES 11 C 267 SER GLY LEU LYS GLN ALA ALA GLU GLU VAL THR LYS GLU SEQRES 12 C 267 PRO ARG GLY LEU LEU MET LEU ALA GLU LEU SER CYS LYS SEQRES 13 C 267 GLY SER LEU SER THR GLY GLU TYR THR LYS GLY THR VAL SEQRES 14 C 267 ASP ILE ALA LYS SER ASP LYS ASP PHE VAL ILE GLY PHE SEQRES 15 C 267 ILE ALA GLN ARG ASP MET GLY GLY ARG ASP GLU GLY TYR SEQRES 16 C 267 ASP TRP LEU ILE MET THR PRO GLY VAL GLY LEU ASP ASP SEQRES 17 C 267 LYS GLY ASP ALA LEU GLY GLN GLN TYR ARG THR VAL ASP SEQRES 18 C 267 ASP VAL VAL SER THR GLY SER ASP ILE ILE ILE VAL GLY SEQRES 19 C 267 ARG GLY LEU PHE ALA LYS GLY ARG ASP ALA LYS VAL GLU SEQRES 20 C 267 GLY GLU ARG TYR ARG LYS ALA GLY TRP GLU ALA TYR LEU SEQRES 21 C 267 ARG ARG CYS GLY GLN GLN ASP SEQRES 1 D 267 MET HIS LYS ALA THR TYR LYS GLU ARG ALA ALA THR HIS SEQRES 2 D 267 PRO SER PRO VAL ALA ALA LYS LEU PHE ASN ILE MET HIS SEQRES 3 D 267 GLU LYS GLN THR ASN LEU CYS ALA SER LEU ASP VAL ARG SEQRES 4 D 267 THR THR LYS GLU LEU LEU GLU LEU VAL GLU ALA LEU GLY SEQRES 5 D 267 PRO LYS ILE CYS LEU LEU LYS THR HIS VAL ASP ILE LEU SEQRES 6 D 267 THR ASP PHE SER MET GLU GLY THR VAL LYS PRO LEU LYS SEQRES 7 D 267 ALA LEU SER ALA LYS TYR ASN PHE LEU LEU PHE GLU ASP SEQRES 8 D 267 ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LEU GLN SEQRES 9 D 267 TYR SER ALA GLY VAL TYR ARG ILE ALA GLU TRP ALA ASP SEQRES 10 D 267 ILE THR ASN ALA HIS GLY VAL VAL GLY PRO GLY ILE VAL SEQRES 11 D 267 SER GLY LEU LYS GLN ALA ALA GLU GLU VAL THR LYS GLU SEQRES 12 D 267 PRO ARG GLY LEU LEU MET LEU ALA GLU LEU SER CYS LYS SEQRES 13 D 267 GLY SER LEU SER THR GLY GLU TYR THR LYS GLY THR VAL SEQRES 14 D 267 ASP ILE ALA LYS SER ASP LYS ASP PHE VAL ILE GLY PHE SEQRES 15 D 267 ILE ALA GLN ARG ASP MET GLY GLY ARG ASP GLU GLY TYR SEQRES 16 D 267 ASP TRP LEU ILE MET THR PRO GLY VAL GLY LEU ASP ASP SEQRES 17 D 267 LYS GLY ASP ALA LEU GLY GLN GLN TYR ARG THR VAL ASP SEQRES 18 D 267 ASP VAL VAL SER THR GLY SER ASP ILE ILE ILE VAL GLY SEQRES 19 D 267 ARG GLY LEU PHE ALA LYS GLY ARG ASP ALA LYS VAL GLU SEQRES 20 D 267 GLY GLU ARG TYR ARG LYS ALA GLY TRP GLU ALA TYR LEU SEQRES 21 D 267 ARG ARG CYS GLY GLN GLN ASP FORMUL 5 HOH *874(H2 O) HELIX 1 1 THR A 5 HIS A 13 1 9 HELIX 2 2 SER A 15 GLN A 29 1 15 HELIX 3 3 THR A 40 GLY A 52 1 13 HELIX 4 4 PRO A 53 ILE A 55 5 3 HELIX 5 5 HIS A 61 LEU A 65 5 5 HELIX 6 6 THR A 73 ASN A 85 1 13 HELIX 7 7 ILE A 97 ALA A 107 1 11 HELIX 8 8 ARG A 111 ALA A 116 1 6 HELIX 9 9 PRO A 127 THR A 141 1 15 HELIX 10 10 THR A 161 LYS A 173 1 13 HELIX 11 11 THR A 219 THR A 226 1 8 HELIX 12 12 GLY A 234 PHE A 238 5 5 HELIX 13 13 ASP A 243 GLY A 264 1 22 HELIX 14 14 THR B 5 HIS B 13 1 9 HELIX 15 15 SER B 15 GLN B 29 1 15 HELIX 16 16 THR B 40 GLY B 52 1 13 HELIX 17 17 PRO B 53 ILE B 55 5 3 HELIX 18 18 HIS B 61 LEU B 65 5 5 HELIX 19 19 THR B 73 TYR B 84 1 12 HELIX 20 20 ILE B 97 ALA B 107 1 11 HELIX 21 21 ARG B 111 TRP B 115 5 5 HELIX 22 22 PRO B 127 THR B 141 1 15 HELIX 23 23 THR B 161 LYS B 173 1 13 HELIX 24 24 GLY B 190 GLY B 194 5 5 HELIX 25 25 THR B 219 THR B 226 1 8 HELIX 26 26 GLY B 234 PHE B 238 5 5 HELIX 27 27 ASP B 243 CYS B 263 1 21 HELIX 28 28 THR C 5 HIS C 13 1 9 HELIX 29 29 SER C 15 GLN C 29 1 15 HELIX 30 30 THR C 40 GLY C 52 1 13 HELIX 31 31 PRO C 53 ILE C 55 5 3 HELIX 32 32 HIS C 61 LEU C 65 5 5 HELIX 33 33 THR C 73 ASN C 85 1 13 HELIX 34 34 ILE C 97 ALA C 107 1 11 HELIX 35 35 ARG C 111 ALA C 116 1 6 HELIX 36 36 PRO C 127 THR C 141 1 15 HELIX 37 37 THR C 161 LYS C 173 1 13 HELIX 38 38 GLY C 190 GLY C 194 5 5 HELIX 39 39 THR C 219 THR C 226 1 8 HELIX 40 40 GLY C 234 PHE C 238 5 5 HELIX 41 41 ASP C 243 GLY C 264 1 22 HELIX 42 42 THR D 5 HIS D 13 1 9 HELIX 43 43 SER D 15 GLN D 29 1 15 HELIX 44 44 THR D 40 GLY D 52 1 13 HELIX 45 45 PRO D 53 ILE D 55 5 3 HELIX 46 46 HIS D 61 LEU D 65 5 5 HELIX 47 47 THR D 73 ASN D 85 1 13 HELIX 48 48 ILE D 97 ALA D 107 1 11 HELIX 49 49 ARG D 111 ALA D 116 1 6 HELIX 50 50 PRO D 127 THR D 141 1 15 HELIX 51 51 THR D 161 LYS D 173 1 13 HELIX 52 52 THR D 219 THR D 226 1 8 HELIX 53 53 GLY D 234 PHE D 238 5 5 HELIX 54 54 ASP D 243 CYS D 263 1 21 SHEET 1 A 9 LEU A 32 SER A 35 0 SHEET 2 A 9 LEU A 57 THR A 60 1 O LEU A 57 N ALA A 34 SHEET 3 A 9 LEU A 87 PHE A 94 1 O LEU A 87 N LEU A 58 SHEET 4 A 9 ILE A 118 HIS A 122 1 N ILE A 118 O LEU A 88 SHEET 5 A 9 GLY A 146 LEU A 150 1 O GLY A 146 N THR A 119 SHEET 6 A 9 VAL A 179 ILE A 183 1 N ILE A 180 O LEU A 147 SHEET 7 A 9 LEU A 198 THR A 201 1 N LEU A 198 O ILE A 180 SHEET 8 A 9 ILE A 230 VAL A 233 1 O ILE A 230 N THR A 201 SHEET 9 A 9 LEU A 32 SER A 35 1 N CYS A 33 O ILE A 231 SHEET 1 B 9 LEU B 32 SER B 35 0 SHEET 2 B 9 LEU B 57 THR B 60 1 O LEU B 57 N ALA B 34 SHEET 3 B 9 LEU B 87 PHE B 94 1 O LEU B 87 N LEU B 58 SHEET 4 B 9 ILE B 118 HIS B 122 1 N ILE B 118 O LEU B 88 SHEET 5 B 9 GLY B 146 LEU B 150 1 O GLY B 146 N THR B 119 SHEET 6 B 9 VAL B 179 ILE B 183 1 N ILE B 180 O LEU B 147 SHEET 7 B 9 LEU B 198 THR B 201 1 N LEU B 198 O ILE B 180 SHEET 8 B 9 ILE B 230 VAL B 233 1 O ILE B 230 N THR B 201 SHEET 9 B 9 LEU B 32 SER B 35 1 N CYS B 33 O ILE B 231 SHEET 1 C 9 LEU C 32 SER C 35 0 SHEET 2 C 9 LEU C 57 THR C 60 1 O LEU C 57 N ALA C 34 SHEET 3 C 9 LEU C 87 PHE C 94 1 O LEU C 87 N LEU C 58 SHEET 4 C 9 ILE C 118 HIS C 122 1 N ILE C 118 O LEU C 88 SHEET 5 C 9 GLY C 146 LEU C 150 1 O GLY C 146 N THR C 119 SHEET 6 C 9 VAL C 179 ILE C 183 1 N ILE C 180 O LEU C 147 SHEET 7 C 9 LEU C 198 PRO C 202 1 N LEU C 198 O ILE C 180 SHEET 8 C 9 ILE C 230 VAL C 233 1 O ILE C 230 N THR C 201 SHEET 9 C 9 LEU C 32 SER C 35 1 N CYS C 33 O ILE C 231 SHEET 1 D 9 LEU D 32 SER D 35 0 SHEET 2 D 9 LEU D 57 THR D 60 1 O LEU D 57 N ALA D 34 SHEET 3 D 9 LEU D 87 PHE D 94 1 O LEU D 87 N LEU D 58 SHEET 4 D 9 ILE D 118 HIS D 122 1 N ILE D 118 O LEU D 88 SHEET 5 D 9 GLY D 146 LEU D 150 1 O GLY D 146 N THR D 119 SHEET 6 D 9 VAL D 179 ILE D 183 1 N ILE D 180 O LEU D 147 SHEET 7 D 9 LEU D 198 THR D 201 1 N LEU D 198 O ILE D 180 SHEET 8 D 9 ILE D 230 VAL D 233 1 O ILE D 230 N THR D 201 SHEET 9 D 9 LEU D 32 SER D 35 1 N CYS D 33 O ILE D 231 CRYST1 90.060 116.217 116.979 90.00 90.00 90.00 P 21 21 21 16 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 0.011104 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008549 0.00000