HEADER LYASE 05-FEB-09 2ZZ1 TITLE SNAPSHOT OF THE REACTION FROM 6-CN-UMP TO BMP CATALYZED BY OROTIDINE TITLE 2 MONOPHOSPHATE DEACARBOXYLASE FROM M. THERMOAUTOTROPHICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A, B; 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: 145262; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE (ODCASE), BARBITURIC ACID KEYWDS 2 RIBOSYL 5'-MONOPHOSPHATE (BMP), 6-CYANOUMP OMP DECARBOXYLASE, OMPDC, KEYWDS 3 OMPDCASE, DECARBOXYLASE, LYASE, PYRIMIDINE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR M.FUJIHASHI,E.F.PAI REVDAT 5 01-NOV-23 2ZZ1 1 REMARK REVDAT 4 10-NOV-21 2ZZ1 1 REMARK SEQADV REVDAT 3 13-JUL-11 2ZZ1 1 VERSN REVDAT 2 15-SEP-09 2ZZ1 1 JRNL REVDAT 1 24-MAR-09 2ZZ1 0 JRNL AUTH M.FUJIHASHI,L.WEI,L.P.KOTRA,E.F.PAI JRNL TITL STRUCTURAL CHARACTERIZATION OF THE MOLECULAR EVENTS DURING A JRNL TITL 2 SLOW SUBSTRATE-PRODUCT TRANSITION IN OROTIDINE JRNL TITL 3 5'-MONOPHOSPHATE DECARBOXYLASE JRNL REF J.MOL.BIOL. V. 387 1199 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19236876 JRNL DOI 10.1016/J.JMB.2009.02.037 REMARK 2 REMARK 2 RESOLUTION. 1.57 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 57489 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : SAME FLAG WITH 1X1Z REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2979 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) : 1.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.61 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4215 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.1650 REMARK 3 BIN FREE R VALUE SET COUNT : 222 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 114 REMARK 3 SOLVENT ATOMS : 287 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 14.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.29000 REMARK 3 B22 (A**2) : 0.26000 REMARK 3 B33 (A**2) : -0.86000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.33000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.074 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.075 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.465 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3547 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4799 ; 1.677 ; 2.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 449 ; 5.480 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 156 ;37.448 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 610 ;12.004 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;18.724 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 550 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2656 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1837 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2419 ; 0.317 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 281 ; 0.122 ; 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): 34 ; 0.198 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.116 ; 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): 2294 ; 1.133 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3586 ; 1.728 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1384 ; 2.980 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1213 ; 4.854 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 5 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 402 A 413 REMARK 3 RESIDUE RANGE : B 401 B 414 REMARK 3 RESIDUE RANGE : A 461 A 461 REMARK 3 ORIGIN FOR THE GROUP (A): 24.8057 -24.8816 14.6731 REMARK 3 T TENSOR REMARK 3 T11: -0.0014 T22: -0.0102 REMARK 3 T33: -0.0081 T12: 0.0055 REMARK 3 T13: 0.0005 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.1697 L22: 0.1315 REMARK 3 L33: 0.2909 L12: -0.0254 REMARK 3 L13: 0.0226 L23: -0.0375 REMARK 3 S TENSOR REMARK 3 S11: 0.0072 S12: 0.0197 S13: -0.0141 REMARK 3 S21: -0.0291 S22: -0.0145 S23: 0.0017 REMARK 3 S31: 0.0533 S32: -0.0011 S33: 0.0073 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 5 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 11 B 225 REMARK 3 RESIDUE RANGE : B 302 B 302 REMARK 3 RESIDUE RANGE : A 421 A 434 REMARK 3 RESIDUE RANGE : B 422 B 433 REMARK 3 RESIDUE RANGE : B 462 B 462 REMARK 3 ORIGIN FOR THE GROUP (A): 24.7937 -10.5043 37.0780 REMARK 3 T TENSOR REMARK 3 T11: -0.0018 T22: -0.0105 REMARK 3 T33: -0.0074 T12: -0.0061 REMARK 3 T13: 0.0048 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.1787 L22: 0.1322 REMARK 3 L33: 0.2900 L12: 0.0234 REMARK 3 L13: -0.0219 L23: -0.0232 REMARK 3 S TENSOR REMARK 3 S11: 0.0100 S12: -0.0185 S13: 0.0138 REMARK 3 S21: 0.0285 S22: -0.0158 S23: 0.0019 REMARK 3 S31: -0.0533 S32: 0.0012 S33: 0.0058 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2ZZ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000028604. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.0-8.5 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) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DEFAULT REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60802 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29600 REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 1X1Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2-1.36M SODIUM CITRATE, 5% DIOXIANE, REMARK 280 PH 6.0-8.5, VAPOR DIFFUSION 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 36.77150 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: 5110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 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 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 SER B 3 REMARK 465 ARG B 4 REMARK 465 ARG B 5 REMARK 465 VAL B 6 REMARK 465 ASP B 7 REMARK 465 VAL B 8 REMARK 465 MET B 9 REMARK 465 ASP B 10 REMARK 465 ARG B 226 REMARK 465 ILE B 227 REMARK 465 PRO B 228 REMARK 465 GLU B 229 REMARK 465 ASP B 230 REMARK 465 PRO B 231 REMARK 465 ALA B 232 REMARK 465 ALA B 233 REMARK 465 ASN B 234 REMARK 465 LYS B 235 REMARK 465 ALA B 236 REMARK 465 ARG B 237 REMARK 465 LYS B 238 REMARK 465 GLU B 239 REMARK 465 ALA B 240 REMARK 465 GLU B 241 REMARK 465 LEU B 242 REMARK 465 ALA B 243 REMARK 465 ALA B 244 REMARK 465 ALA B 245 REMARK 465 THR B 246 REMARK 465 ALA B 247 REMARK 465 GLU B 248 REMARK 465 GLN B 249 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 118 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 163 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 118 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 118 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG B 160 NE - CZ - NH2 ANGL. DEV. = -3.1 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 ALA A 74 45.38 -151.58 REMARK 500 THR A 124 -89.41 -97.80 REMARK 500 PHE A 134 -41.34 -132.45 REMARK 500 ALA B 74 47.47 -152.05 REMARK 500 THR B 124 -90.22 -97.41 REMARK 500 PHE B 134 -39.33 -132.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 BMP 301(302) AND 6CN 303(304) ARE IN ALTERNATE CONFORMATIONS OF REMARK 600 EACH OTHER. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 6CN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMP B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 6CN B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 313 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2E6Y RELATED DB: PDB REMARK 900 THE SAME ENZYME FROM THE SAME SOURCE REMARK 900 RELATED ID: 1X1Z RELATED DB: PDB REMARK 900 THE SAME ENZYME FROM THE SAME SOURCE REMARK 900 RELATED ID: 1LP6 RELATED DB: PDB REMARK 900 THE SAME ENZYME FROM THE SAME SOURCE REMARK 900 RELATED ID: 1LOS RELATED DB: PDB REMARK 900 THE SAME ENZYME FROM THE SAME SOURCE REMARK 900 RELATED ID: 1LOR RELATED DB: PDB REMARK 900 THE SAME ENZYME FROM THE SAME SOURCE REMARK 900 RELATED ID: 1DV7 RELATED DB: PDB REMARK 900 THE SAME ENZYME FROM THE SAME SOURCE REMARK 900 RELATED ID: 2ZZ2 RELATED DB: PDB REMARK 900 RELATED ID: 2ZZ3 RELATED DB: PDB REMARK 900 RELATED ID: 2ZZ4 RELATED DB: PDB REMARK 900 RELATED ID: 2ZZ5 RELATED DB: PDB REMARK 900 RELATED ID: 2ZZ6 RELATED DB: PDB REMARK 900 RELATED ID: 2ZZ7 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO DEPOSITORS, PRO101 IS CORRECT REMARK 999 AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. REMARK 999 DEPOSITORS SEQUENCED THE GENOME FROM M. THERMOAUTOTROPHICUM REMARK 999 AND CONFIRMD IT IS PRO. DBREF 2ZZ1 A 1 228 UNP O26232 PYRF_METTH 1 228 DBREF 2ZZ1 B 1 228 UNP O26232 PYRF_METTH 1 228 SEQADV 2ZZ1 GLY A -2 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 SER A -1 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 HIS A 0 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 PRO A 101 UNP O26232 ARG 101 SEE REMARK 999 SEQADV 2ZZ1 ARG A 226 UNP O26232 LEU 226 ENGINEERED MUTATION SEQADV 2ZZ1 ILE A 227 UNP O26232 ASN 227 ENGINEERED MUTATION SEQADV 2ZZ1 GLU A 229 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ASP A 230 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 PRO A 231 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA A 232 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA A 233 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ASN A 234 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 LYS A 235 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA A 236 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ARG A 237 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 LYS A 238 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 GLU A 239 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA A 240 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 GLU A 241 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 LEU A 242 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA A 243 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA A 244 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA A 245 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 THR A 246 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA A 247 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 GLU A 248 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 GLN A 249 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 GLY B -2 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 SER B -1 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 HIS B 0 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 PRO B 101 UNP O26232 ARG 101 SEE REMARK 999 SEQADV 2ZZ1 ARG B 226 UNP O26232 LEU 226 ENGINEERED MUTATION SEQADV 2ZZ1 ILE B 227 UNP O26232 ASN 227 ENGINEERED MUTATION SEQADV 2ZZ1 GLU B 229 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ASP B 230 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 PRO B 231 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA B 232 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA B 233 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ASN B 234 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 LYS B 235 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA B 236 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ARG B 237 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 LYS B 238 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 GLU B 239 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA B 240 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 GLU B 241 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 LEU B 242 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA B 243 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA B 244 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA B 245 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 THR B 246 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 ALA B 247 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 GLU B 248 UNP O26232 EXPRESSION TAG SEQADV 2ZZ1 GLN B 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 SEQRES 1 B 252 GLY SER HIS MET ARG SER ARG ARG VAL ASP VAL MET ASP SEQRES 2 B 252 VAL MET ASN ARG LEU ILE LEU ALA MET ASP LEU MET ASN SEQRES 3 B 252 ARG ASP ASP ALA LEU ARG VAL THR GLY GLU VAL ARG GLU SEQRES 4 B 252 TYR ILE ASP THR VAL LYS ILE GLY TYR PRO LEU VAL LEU SEQRES 5 B 252 SER GLU GLY MET ASP ILE ILE ALA GLU PHE ARG LYS ARG SEQRES 6 B 252 PHE GLY CYS ARG ILE ILE ALA ASP PHE LYS VAL ALA ASP SEQRES 7 B 252 ILE PRO GLU THR ASN GLU LYS ILE CYS ARG ALA THR PHE SEQRES 8 B 252 LYS ALA GLY ALA ASP ALA ILE ILE VAL HIS GLY PHE PRO SEQRES 9 B 252 GLY ALA ASP SER VAL ARG ALA CYS LEU ASN VAL ALA GLU SEQRES 10 B 252 GLU MET GLY ARG GLU VAL PHE LEU LEU THR GLU MET SER SEQRES 11 B 252 HIS PRO GLY ALA GLU MET PHE ILE GLN GLY ALA ALA ASP SEQRES 12 B 252 GLU ILE ALA ARG MET GLY VAL ASP LEU GLY VAL LYS ASN SEQRES 13 B 252 TYR VAL GLY PRO SER THR ARG PRO GLU ARG LEU SER ARG SEQRES 14 B 252 LEU ARG GLU ILE ILE GLY GLN ASP SER PHE LEU ILE SER SEQRES 15 B 252 PRO GLY VAL GLY ALA GLN GLY GLY ASP PRO GLY GLU THR SEQRES 16 B 252 LEU ARG PHE ALA ASP ALA ILE ILE VAL GLY ARG SER ILE SEQRES 17 B 252 TYR LEU ALA ASP ASN PRO ALA ALA ALA ALA ALA GLY ILE SEQRES 18 B 252 ILE GLU SER ILE LYS ASP LEU ARG ILE PRO GLU ASP PRO SEQRES 19 B 252 ALA ALA ASN LYS ALA ARG LYS GLU ALA GLU LEU ALA ALA SEQRES 20 B 252 ALA THR ALA GLU GLN HET BMP A 301 22 HET 6CN A 303 23 HET GOL A 311 6 HET GOL A 312 6 HET GOL A 314 6 HET BMP B 302 22 HET 6CN B 304 23 HET GOL B 313 6 HETNAM BMP 6-HYDROXYURIDINE-5'-PHOSPHATE HETNAM 6CN 6-CYANOURIDINE 5'-PHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 BMP 2(C9 H13 N2 O10 P) FORMUL 4 6CN 2(C10 H12 N3 O9 P) FORMUL 5 GOL 4(C3 H8 O3) FORMUL 11 HOH *287(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 LEU A 225 1 16 HELIX 14 14 VAL B 11 ASN B 13 5 3 HELIX 15 15 ASN B 23 ARG B 35 1 13 HELIX 16 16 GLU B 36 ILE B 38 5 3 HELIX 17 17 TYR B 45 GLY B 52 1 8 HELIX 18 18 MET B 53 GLY B 64 1 12 HELIX 19 19 ILE B 76 ALA B 90 1 15 HELIX 20 20 GLY B 102 GLY B 117 1 16 HELIX 21 21 HIS B 128 MET B 133 5 6 HELIX 22 22 PHE B 134 GLY B 150 1 17 HELIX 23 23 ARG B 160 GLY B 172 1 13 HELIX 24 24 ASP B 188 LEU B 193 1 6 HELIX 25 25 GLY B 202 LEU B 207 1 6 HELIX 26 26 ASN B 210 LEU B 225 1 16 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 SHEET 1 B 9 LEU B 15 MET B 19 0 SHEET 2 B 9 THR B 40 GLY B 44 1 O LYS B 42 N LEU B 17 SHEET 3 B 9 ARG B 66 VAL B 73 1 O ARG B 66 N VAL B 41 SHEET 4 B 9 ALA B 94 HIS B 98 1 O ALA B 94 N ALA B 69 SHEET 5 B 9 GLU B 119 LEU B 123 1 O LEU B 123 N VAL B 97 SHEET 6 B 9 ASN B 153 VAL B 155 1 O ASN B 153 N LEU B 122 SHEET 7 B 9 PHE B 176 SER B 179 1 O ILE B 178 N TYR B 154 SHEET 8 B 9 ALA B 198 VAL B 201 1 O ILE B 200 N SER B 179 SHEET 9 B 9 LEU B 15 MET B 19 1 N ILE B 16 O ILE B 199 SITE 1 AC1 20 ASP A 20 LYS A 42 ASP A 70 LYS A 72 SITE 2 AC1 20 MET A 126 SER A 127 PRO A 180 GLN A 185 SITE 3 AC1 20 GLY A 202 ARG A 203 HOH A 402 HOH A 403 SITE 4 AC1 20 HOH A 406 HOH A 407 HOH A 408 HOH A 411 SITE 5 AC1 20 HOH A 461 ASP B 75 ILE B 76 THR B 79 SITE 1 AC2 21 ASP A 20 LYS A 42 ASP A 70 LYS A 72 SITE 2 AC2 21 ILE A 96 MET A 126 SER A 127 PRO A 180 SITE 3 AC2 21 GLN A 185 GLY A 202 ARG A 203 HOH A 402 SITE 4 AC2 21 HOH A 403 HOH A 406 HOH A 407 HOH A 408 SITE 5 AC2 21 HOH A 411 HOH A 461 ASP B 75 ILE B 76 SITE 6 AC2 21 THR B 79 SITE 1 AC3 8 GLU A 33 ASN A 210 HOH A 522 HOH A 528 SITE 2 AC3 8 HOH A 717 THR B 159 PRO B 161 GLY B 186 SITE 1 AC4 6 THR A 159 PRO A 161 GLY A 186 ASN B 210 SITE 2 AC4 6 HOH B 519 HOH B 530 SITE 1 AC5 7 ALA A 208 ASP A 209 ASN A 210 ALA A 213 SITE 2 AC5 7 ALA A 214 HOH A 565 GLU B 162 SITE 1 AC6 20 ASP A 75 ILE A 76 THR A 79 ASP B 20 SITE 2 AC6 20 LYS B 42 ASP B 70 LYS B 72 MET B 126 SITE 3 AC6 20 SER B 127 PRO B 180 GLN B 185 GLY B 202 SITE 4 AC6 20 ARG B 203 HOH B 422 HOH B 423 HOH B 426 SITE 5 AC6 20 HOH B 427 HOH B 428 HOH B 431 HOH B 462 SITE 1 AC7 21 ASP A 75 ILE A 76 THR A 79 ASP B 20 SITE 2 AC7 21 LYS B 42 ASP B 70 LYS B 72 ILE B 96 SITE 3 AC7 21 MET B 126 SER B 127 PRO B 180 GLN B 185 SITE 4 AC7 21 GLY B 202 ARG B 203 HOH B 422 HOH B 423 SITE 5 AC7 21 HOH B 426 HOH B 427 HOH B 428 HOH B 431 SITE 6 AC7 21 HOH B 462 SITE 1 AC8 6 GLU A 162 ALA B 208 ASP B 209 ASN B 210 SITE 2 AC8 6 ALA B 213 ALA B 214 CRYST1 58.024 73.543 59.331 90.00 119.29 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 0.017234 0.000000 0.009667 0.00000 SCALE2 0.000000 0.013597 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019325 0.00000