HEADER LYASE 17-OCT-13 3WJW TITLE WILD-TYPE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM M. TITLE 2 THERMOAUTOTROPHICUS COMPLEXED WITH 6-METHYL-UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OMP DECARBOXYLASE, OMPDCASE, OMPDECASE; COMPND 5 EC: 4.1.1.23; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS; SOURCE 3 ORGANISM_TAXID: 187420; SOURCE 4 STRAIN: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / DELTA H; SOURCE 5 GENE: PYRF, MTH_129; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS TIM BARREL, DECARBOXYLASE, PYRIMIDINE BIOSYNTHESIS, PROTEIN-LIGAND KEYWDS 2 COMPLEX, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.FUJIHASHI,S.KURODA,E.F.PAI,K.MIKI REVDAT 2 08-NOV-23 3WJW 1 REMARK SEQADV REVDAT 1 04-DEC-13 3WJW 0 JRNL AUTH M.FUJIHASHI,T.ISHIDA,S.KURODA,L.P.KOTRA,E.F.PAI,K.MIKI JRNL TITL SUBSTRATE DISTORTION CONTRIBUTES TO THE CATALYSIS OF JRNL TITL 2 OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE. JRNL REF J.AM.CHEM.SOC. V. 135 17432 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 24151964 JRNL DOI 10.1021/JA408197K REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30105 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1487 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) : 1.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.63 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2109 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.1690 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.2140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1630 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48000 REMARK 3 B22 (A**2) : -1.01000 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): 0.079 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.525 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1760 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2389 ; 1.593 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 231 ; 5.635 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;40.572 ;23.077 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 302 ;13.260 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;20.373 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 268 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1350 ; 0.013 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1113 ; 0.981 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1795 ; 1.699 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 647 ; 2.915 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 593 ; 4.871 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 225 REMARK 3 RESIDUE RANGE : A 301 A 301 REMARK 3 RESIDUE RANGE : A 401 A 553 REMARK 3 ORIGIN FOR THE GROUP (A): 18.6002 40.5617 29.7071 REMARK 3 T TENSOR REMARK 3 T11: 0.0314 T22: 0.0220 REMARK 3 T33: 0.0083 T12: 0.0011 REMARK 3 T13: -0.0069 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.6800 L22: 1.0246 REMARK 3 L33: 0.5138 L12: -0.0680 REMARK 3 L13: -0.0086 L23: -0.1095 REMARK 3 S TENSOR REMARK 3 S11: 0.0119 S12: 0.0434 S13: -0.0696 REMARK 3 S21: -0.1126 S22: 0.0020 S23: 0.0200 REMARK 3 S31: 0.0751 S32: -0.0032 S33: -0.0139 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: NULL REMARK 4 REMARK 4 3WJW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000096427. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 : 30174 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 51.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5 REMARK 200 STARTING MODEL: 3WJY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, PH 6, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K 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 36.75400 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 36.75400 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 29.01250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.78650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.01250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.78650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.75400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.01250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.78650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 36.75400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.01250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.78650 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: 3390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 103.57300 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 73.50800 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 ARG A 5 REMARK 465 VAL A 6 REMARK 465 ASP A 7 REMARK 465 VAL A 8 REMARK 465 MET A 9 REMARK 465 ASP A 10 REMARK 465 ARG A 226 REMARK 465 ILE A 227 REMARK 465 PRO A 228 REMARK 465 GLU A 229 REMARK 465 ASP A 230 REMARK 465 PRO A 231 REMARK 465 ALA A 232 REMARK 465 ALA A 233 REMARK 465 ASN A 234 REMARK 465 LYS A 235 REMARK 465 ALA A 236 REMARK 465 ARG A 237 REMARK 465 LYS A 238 REMARK 465 GLU A 239 REMARK 465 ALA A 240 REMARK 465 GLU A 241 REMARK 465 LEU A 242 REMARK 465 ALA A 243 REMARK 465 ALA A 244 REMARK 465 ALA A 245 REMARK 465 THR A 246 REMARK 465 ALA A 247 REMARK 465 GLU A 248 REMARK 465 GLN A 249 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 74 43.16 -149.47 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 U6M A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WJX RELATED DB: PDB REMARK 900 RELATED ID: 3WJY RELATED DB: PDB REMARK 900 RELATED ID: 3WJZ RELATED DB: PDB REMARK 900 RELATED ID: 3WK0 RELATED DB: PDB REMARK 900 RELATED ID: 3WK1 RELATED DB: PDB REMARK 900 RELATED ID: 3WK2 RELATED DB: PDB REMARK 900 RELATED ID: 3WK3 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY REMARK 999 INCORRECT AT THIS POSITION. DEPOSITORS SEQUENCED THE GENOME FROM M. REMARK 999 THERMOAUTOTROPHICUS AND CONFIRMED IT IS PRO. DBREF 3WJW A 1 228 UNP O26232 PYRF_METTH 1 228 SEQADV 3WJW GLY A -2 UNP O26232 EXPRESSION TAG SEQADV 3WJW SER A -1 UNP O26232 EXPRESSION TAG SEQADV 3WJW HIS A 0 UNP O26232 EXPRESSION TAG SEQADV 3WJW PRO A 101 UNP O26232 ARG 101 SEE REMARK 999 SEQADV 3WJW ARG A 226 UNP O26232 LEU 226 ENGINEERED MUTATION SEQADV 3WJW ILE A 227 UNP O26232 ASN 227 ENGINEERED MUTATION SEQADV 3WJW GLU A 229 UNP O26232 EXPRESSION TAG SEQADV 3WJW ASP A 230 UNP O26232 EXPRESSION TAG SEQADV 3WJW PRO A 231 UNP O26232 EXPRESSION TAG SEQADV 3WJW ALA A 232 UNP O26232 EXPRESSION TAG SEQADV 3WJW ALA A 233 UNP O26232 EXPRESSION TAG SEQADV 3WJW ASN A 234 UNP O26232 EXPRESSION TAG SEQADV 3WJW LYS A 235 UNP O26232 EXPRESSION TAG SEQADV 3WJW ALA A 236 UNP O26232 EXPRESSION TAG SEQADV 3WJW ARG A 237 UNP O26232 EXPRESSION TAG SEQADV 3WJW LYS A 238 UNP O26232 EXPRESSION TAG SEQADV 3WJW GLU A 239 UNP O26232 EXPRESSION TAG SEQADV 3WJW ALA A 240 UNP O26232 EXPRESSION TAG SEQADV 3WJW GLU A 241 UNP O26232 EXPRESSION TAG SEQADV 3WJW LEU A 242 UNP O26232 EXPRESSION TAG SEQADV 3WJW ALA A 243 UNP O26232 EXPRESSION TAG SEQADV 3WJW ALA A 244 UNP O26232 EXPRESSION TAG SEQADV 3WJW ALA A 245 UNP O26232 EXPRESSION TAG SEQADV 3WJW THR A 246 UNP O26232 EXPRESSION TAG SEQADV 3WJW ALA A 247 UNP O26232 EXPRESSION TAG SEQADV 3WJW GLU A 248 UNP O26232 EXPRESSION TAG SEQADV 3WJW GLN A 249 UNP O26232 EXPRESSION TAG SEQRES 1 A 252 GLY SER HIS MET ARG SER ARG ARG VAL ASP VAL MET ASP SEQRES 2 A 252 VAL MET ASN ARG LEU ILE LEU ALA MET ASP LEU MET ASN SEQRES 3 A 252 ARG ASP ASP ALA LEU ARG VAL THR GLY GLU VAL ARG GLU SEQRES 4 A 252 TYR ILE ASP THR VAL LYS ILE GLY TYR PRO LEU VAL LEU SEQRES 5 A 252 SER GLU GLY MET ASP ILE ILE ALA GLU PHE ARG LYS ARG SEQRES 6 A 252 PHE GLY CYS ARG ILE ILE ALA ASP PHE LYS VAL ALA ASP SEQRES 7 A 252 ILE PRO GLU THR ASN GLU LYS ILE CYS ARG ALA THR PHE SEQRES 8 A 252 LYS ALA GLY ALA ASP ALA ILE ILE VAL HIS GLY PHE PRO SEQRES 9 A 252 GLY ALA ASP SER VAL ARG ALA CYS LEU ASN VAL ALA GLU SEQRES 10 A 252 GLU MET GLY ARG GLU VAL PHE LEU LEU THR GLU MET SER SEQRES 11 A 252 HIS PRO GLY ALA GLU MET PHE ILE GLN GLY ALA ALA ASP SEQRES 12 A 252 GLU ILE ALA ARG MET GLY VAL ASP LEU GLY VAL LYS ASN SEQRES 13 A 252 TYR VAL GLY PRO SER THR ARG PRO GLU ARG LEU SER ARG SEQRES 14 A 252 LEU ARG GLU ILE ILE GLY GLN ASP SER PHE LEU ILE SER SEQRES 15 A 252 PRO GLY VAL GLY ALA GLN GLY GLY ASP PRO GLY GLU THR SEQRES 16 A 252 LEU ARG PHE ALA ASP ALA ILE ILE VAL GLY ARG SER ILE SEQRES 17 A 252 TYR LEU ALA ASP ASN PRO ALA ALA ALA ALA ALA GLY ILE SEQRES 18 A 252 ILE GLU SER ILE LYS ASP LEU ARG ILE PRO GLU ASP PRO SEQRES 19 A 252 ALA ALA ASN LYS ALA ARG LYS GLU ALA GLU LEU ALA ALA SEQRES 20 A 252 ALA THR ALA GLU GLN HET U6M A 301 22 HETNAM U6M 6-METHYLURIDINE 5'-(DIHYDROGEN PHOSPHATE) FORMUL 2 U6M C10 H15 N2 O9 P FORMUL 3 HOH *153(H2 O) HELIX 1 1 VAL A 11 ASN A 13 5 3 HELIX 2 2 ASN A 23 ARG A 35 1 13 HELIX 3 3 GLU A 36 ILE A 38 5 3 HELIX 4 4 TYR A 45 GLY A 52 1 8 HELIX 5 5 MET A 53 GLY A 64 1 12 HELIX 6 6 ILE A 76 ALA A 90 1 15 HELIX 7 7 GLY A 102 GLY A 117 1 16 HELIX 8 8 HIS A 128 MET A 133 5 6 HELIX 9 9 PHE A 134 GLY A 150 1 17 HELIX 10 10 ARG A 160 GLY A 172 1 13 HELIX 11 11 ASP A 188 LEU A 193 1 6 HELIX 12 12 GLY A 202 LEU A 207 1 6 HELIX 13 13 ASN A 210 ASP A 224 1 15 SHEET 1 A 9 LEU A 15 MET A 19 0 SHEET 2 A 9 THR A 40 GLY A 44 1 O LYS A 42 N LEU A 17 SHEET 3 A 9 ARG A 66 VAL A 73 1 O ARG A 66 N VAL A 41 SHEET 4 A 9 ALA A 94 HIS A 98 1 O ALA A 94 N ALA A 69 SHEET 5 A 9 GLU A 119 LEU A 123 1 O LEU A 123 N VAL A 97 SHEET 6 A 9 ASN A 153 VAL A 155 1 O ASN A 153 N LEU A 122 SHEET 7 A 9 PHE A 176 SER A 179 1 O PHE A 176 N TYR A 154 SHEET 8 A 9 ALA A 198 VAL A 201 1 O ILE A 200 N SER A 179 SHEET 9 A 9 LEU A 15 MET A 19 1 N ILE A 16 O ILE A 199 SITE 1 AC1 19 ASP A 20 LYS A 42 ASP A 70 LYS A 72 SITE 2 AC1 19 ASP A 75 ILE A 76 THR A 79 MET A 126 SITE 3 AC1 19 SER A 127 PRO A 180 GLN A 185 GLY A 202 SITE 4 AC1 19 ARG A 203 HOH A 402 HOH A 403 HOH A 406 SITE 5 AC1 19 HOH A 407 HOH A 408 HOH A 411 CRYST1 58.025 103.573 73.508 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 0.017234 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009655 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013604 0.00000