HEADER OXIDOREDUCTASE 04-MAY-07 2PRL TITLE THE STRUCTURES OF APO- AND INHIBITOR BOUND HUMAN DIHYDROOROTATE TITLE 2 DEHYDROGENASE REVEAL CONFORMATIONAL FLEXIBILITY WITHIN THE INHIBITOR TITLE 3 BINDING SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: (DIHYDROOROTATE OXIDASE; DHODEHASE; COMPND 5 EC: 1.3.99.11; 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 CELLULAR_LOCATION: MITOCHONDRIA; SOURCE 6 GENE: DHODH; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-19B KEYWDS PROTEIN INHIBITOR COMPLEX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.WALSE,V.T.DUFE,S.AL-KARADAGHI REVDAT 6 30-AUG-23 2PRL 1 REMARK REVDAT 5 07-MAR-18 2PRL 1 REMARK REVDAT 4 13-JUL-11 2PRL 1 VERSN REVDAT 3 23-DEC-08 2PRL 1 JRNL VERSN REVDAT 2 03-JUN-08 2PRL 1 DBREF REVDAT 1 20-MAY-08 2PRL 0 JRNL AUTH B.WALSE,V.T.DUFE,B.SVENSSON,I.FRITZSON,L.DAHLBERG, JRNL AUTH 2 A.KHAIROULLINA,U.WELLMAR,S.AL-KARADAGHI JRNL TITL THE STRUCTURES OF HUMAN DIHYDROOROTATE DEHYDROGENASE WITH JRNL TITL 2 AND WITHOUT INHIBITOR REVEAL CONFORMATIONAL FLEXIBILITY IN JRNL TITL 3 THE INHIBITOR AND SUBSTRATE BINDING SITES JRNL REF BIOCHEMISTRY V. 47 8929 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18672895 JRNL DOI 10.1021/BI8003318 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 31888 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1678 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2311 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1640 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.2100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2805 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 94 REMARK 3 SOLVENT ATOMS : 231 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 22.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.16000 REMARK 3 B22 (A**2) : 0.16000 REMARK 3 B33 (A**2) : -0.25000 REMARK 3 B12 (A**2) : 0.08000 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): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.642 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2963 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4013 ; 1.298 ; 2.018 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 376 ; 5.696 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;35.984 ;22.992 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;12.664 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;18.191 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 442 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2250 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1499 ; 0.191 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2028 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 273 ; 0.126 ; 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): 50 ; 0.208 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.135 ; 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): 1897 ; 0.487 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2929 ; 0.755 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1228 ; 1.270 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1079 ; 2.081 ; 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 : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 30 A 36 REMARK 3 ORIGIN FOR THE GROUP (A): 53.2044 57.1639 -6.2084 REMARK 3 T TENSOR REMARK 3 T11: -0.0686 T22: 0.1551 REMARK 3 T33: 0.1455 T12: -0.0129 REMARK 3 T13: 0.0818 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 33.1641 L22: 52.1721 REMARK 3 L33: 27.0657 L12: 13.0061 REMARK 3 L13: -13.8311 L23: -12.9519 REMARK 3 S TENSOR REMARK 3 S11: 0.1735 S12: 0.2722 S13: 1.3518 REMARK 3 S21: -0.2463 S22: -0.0943 S23: -3.5574 REMARK 3 S31: -0.0898 S32: 2.5988 S33: -0.0792 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 37 A 77 REMARK 3 ORIGIN FOR THE GROUP (A): 53.6477 48.2138 -1.6786 REMARK 3 T TENSOR REMARK 3 T11: -0.0357 T22: 0.0082 REMARK 3 T33: -0.0008 T12: -0.0318 REMARK 3 T13: 0.0342 T23: 0.0497 REMARK 3 L TENSOR REMARK 3 L11: 2.1529 L22: 1.0598 REMARK 3 L33: 3.5836 L12: 0.4734 REMARK 3 L13: 0.6029 L23: 0.7746 REMARK 3 S TENSOR REMARK 3 S11: 0.0216 S12: 0.0988 S13: 0.2843 REMARK 3 S21: -0.1790 S22: -0.0227 S23: -0.2891 REMARK 3 S31: -0.4038 S32: 0.3867 S33: 0.0011 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 78 A 148 REMARK 3 ORIGIN FOR THE GROUP (A): 46.9079 40.9483 7.9028 REMARK 3 T TENSOR REMARK 3 T11: 0.0198 T22: 0.0631 REMARK 3 T33: 0.0261 T12: -0.0102 REMARK 3 T13: -0.0002 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 1.0480 L22: 0.6852 REMARK 3 L33: 0.7929 L12: -0.1148 REMARK 3 L13: 0.4848 L23: 0.0295 REMARK 3 S TENSOR REMARK 3 S11: -0.0093 S12: -0.0007 S13: 0.0480 REMARK 3 S21: 0.0137 S22: -0.0104 S23: -0.0484 REMARK 3 S31: -0.0332 S32: 0.1495 S33: 0.0197 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 149 A 216 REMARK 3 ORIGIN FOR THE GROUP (A): 49.9904 34.6265 18.5304 REMARK 3 T TENSOR REMARK 3 T11: 0.0178 T22: 0.0579 REMARK 3 T33: 0.0050 T12: 0.0054 REMARK 3 T13: -0.0081 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 1.7204 L22: 0.8777 REMARK 3 L33: 1.3534 L12: -0.4766 REMARK 3 L13: 0.1076 L23: -0.4031 REMARK 3 S TENSOR REMARK 3 S11: -0.0133 S12: -0.0477 S13: -0.0973 REMARK 3 S21: 0.0372 S22: -0.0425 S23: -0.0452 REMARK 3 S31: 0.1299 S32: -0.0067 S33: 0.0559 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 217 A 231 REMARK 3 ORIGIN FOR THE GROUP (A): 32.4169 26.6260 15.6801 REMARK 3 T TENSOR REMARK 3 T11: 0.1176 T22: 0.2835 REMARK 3 T33: 0.0333 T12: -0.0021 REMARK 3 T13: -0.0298 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 9.7680 L22: 0.9619 REMARK 3 L33: 17.8493 L12: 2.2520 REMARK 3 L13: -12.9093 L23: -3.5670 REMARK 3 S TENSOR REMARK 3 S11: -0.3820 S12: 1.3266 S13: -0.6898 REMARK 3 S21: -0.7902 S22: 0.1544 S23: 0.0085 REMARK 3 S31: 1.1415 S32: -1.6280 S33: 0.2276 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 232 A 271 REMARK 3 ORIGIN FOR THE GROUP (A): 36.3230 34.3037 23.2697 REMARK 3 T TENSOR REMARK 3 T11: 0.0027 T22: 0.0446 REMARK 3 T33: 0.0046 T12: 0.0014 REMARK 3 T13: 0.0272 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 3.2327 L22: 0.4890 REMARK 3 L33: 2.2011 L12: -0.4140 REMARK 3 L13: 1.6326 L23: -0.3666 REMARK 3 S TENSOR REMARK 3 S11: -0.0570 S12: -0.1549 S13: -0.1424 REMARK 3 S21: 0.0318 S22: 0.0510 S23: 0.0330 REMARK 3 S31: 0.0415 S32: -0.1573 S33: 0.0060 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 272 A 346 REMARK 3 ORIGIN FOR THE GROUP (A): 31.8329 42.3611 8.0704 REMARK 3 T TENSOR REMARK 3 T11: -0.0050 T22: 0.0401 REMARK 3 T33: 0.0233 T12: 0.0137 REMARK 3 T13: -0.0098 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.8025 L22: 0.6305 REMARK 3 L33: 1.0815 L12: -0.2525 REMARK 3 L13: 0.1120 L23: 0.0956 REMARK 3 S TENSOR REMARK 3 S11: -0.0302 S12: -0.1193 S13: -0.0153 REMARK 3 S21: 0.0151 S22: 0.0095 S23: 0.0575 REMARK 3 S31: -0.0035 S32: -0.0704 S33: 0.0207 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 347 A 396 REMARK 3 ORIGIN FOR THE GROUP (A): 37.9272 54.6673 7.9272 REMARK 3 T TENSOR REMARK 3 T11: 0.0398 T22: 0.0285 REMARK 3 T33: 0.0412 T12: 0.0041 REMARK 3 T13: -0.0312 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 1.1742 L22: 1.5142 REMARK 3 L33: 1.2790 L12: -0.2477 REMARK 3 L13: -0.0917 L23: 0.1964 REMARK 3 S TENSOR REMARK 3 S11: -0.0128 S12: -0.0247 S13: 0.1932 REMARK 3 S21: -0.0005 S22: -0.0076 S23: -0.0804 REMARK 3 S31: -0.2450 S32: -0.0025 S33: 0.0203 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042706. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-04; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; NULL REMARK 200 RADIATION SOURCE : MAX II; NULL REMARK 200 BEAMLINE : I711; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.092; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; NULL REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33570 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 18.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1700 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) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1D3G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROPS WERE FORMED BY MIXING EQUAL REMARK 280 AMOUNTS OF 18-24 MG/ML PROTEIN IN 100 MM HEPES PH 7.0, 400 MM REMARK 280 NACL, 30% GLYCEROL, 1 MM EDTA AND 10 MM N,N- DIMETHYLUNDECYLAMIN- REMARK 280 N-OXIDE (C11DAO) WITH A PRECIPITANT SOLUTION OF 0.1 M ACETATE PH REMARK 280 4.8 40 MM C11DAO, 20.8 MM N,-DIMETHYLDECYLAMINE-N-OXIDE (DDAO), REMARK 280 2 MM DIHYDROOROTATE (DHO) THE HANGING DROPS WERE INCUBATED REMARK 280 AGAINST 0.5 ML RESERVOIR OF 0.1 M ACETATE PH 4.8, 1.6-2.2 M REMARK 280 AMMONIUM SULFATE AND 30% GLYCEROL., VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.38000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.69000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 40.69000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 81.38000 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 300 REMARK: BIOLOGICAL UNIT IS A MONOMER 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 155 CB OG REMARK 480 SER A 188 CB OG REMARK 480 SER A 313 CB OG 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 SER A 313 CA SER A 313 CB 0.109 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 SER A 155 N - CA - CB ANGL. DEV. = 9.9 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 ASP A 34 119.73 165.42 REMARK 500 HIS A 41 -59.81 -129.10 REMARK 500 ASP A 99 77.42 -109.41 REMARK 500 ASN A 284 -172.93 -69.63 REMARK 500 TYR A 356 -62.72 -138.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 33 ASP A 34 -105.03 REMARK 500 PRO A 216 ASN A 217 -148.11 REMARK 500 GLY A 226 LYS A 227 -149.54 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 SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 398 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ORO A 399 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R2C A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDQ A 700 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PRH RELATED DB: PDB REMARK 900 RELATED ID: 2PRM RELATED DB: PDB REMARK 900 RELATED ID: 1D3G RELATED DB: PDB DBREF 2PRL A 30 396 UNP Q02127 PYRD_HUMAN 29 395 SEQRES 1 A 367 MET ALA THR GLY ASP GLU ARG PHE TYR ALA GLU HIS LEU SEQRES 2 A 367 MET PRO THR LEU GLN GLY LEU LEU ASP PRO GLU SER ALA SEQRES 3 A 367 HIS ARG LEU ALA VAL ARG PHE THR SER LEU GLY LEU LEU SEQRES 4 A 367 PRO ARG ALA ARG PHE GLN ASP SER ASP MET LEU GLU VAL SEQRES 5 A 367 ARG VAL LEU GLY HIS LYS PHE ARG ASN PRO VAL GLY ILE SEQRES 6 A 367 ALA ALA GLY PHE ASP LYS HIS GLY GLU ALA VAL ASP GLY SEQRES 7 A 367 LEU TYR LYS MET GLY PHE GLY PHE VAL GLU ILE GLY SER SEQRES 8 A 367 VAL THR PRO LYS PRO GLN GLU GLY ASN PRO ARG PRO ARG SEQRES 9 A 367 VAL PHE ARG LEU PRO GLU ASP GLN ALA VAL ILE ASN ARG SEQRES 10 A 367 TYR GLY PHE ASN SER HIS GLY LEU SER VAL VAL GLU HIS SEQRES 11 A 367 ARG LEU ARG ALA ARG GLN GLN LYS GLN ALA LYS LEU THR SEQRES 12 A 367 GLU ASP GLY LEU PRO LEU GLY VAL ASN LEU GLY LYS ASN SEQRES 13 A 367 LYS THR SER VAL ASP ALA ALA GLU ASP TYR ALA GLU GLY SEQRES 14 A 367 VAL ARG VAL LEU GLY PRO LEU ALA ASP TYR LEU VAL VAL SEQRES 15 A 367 ASN VAL SER SER PRO ASN THR ALA GLY LEU ARG SER LEU SEQRES 16 A 367 GLN GLY LYS ALA GLU LEU ARG ARG LEU LEU THR LYS VAL SEQRES 17 A 367 LEU GLN GLU ARG ASP GLY LEU ARG ARG VAL HIS ARG PRO SEQRES 18 A 367 ALA VAL LEU VAL LYS ILE ALA PRO ASP LEU THR SER GLN SEQRES 19 A 367 ASP LYS GLU ASP ILE ALA SER VAL VAL LYS GLU LEU GLY SEQRES 20 A 367 ILE ASP GLY LEU ILE VAL THR ASN THR THR VAL SER ARG SEQRES 21 A 367 PRO ALA GLY LEU GLN GLY ALA LEU ARG SER GLU THR GLY SEQRES 22 A 367 GLY LEU SER GLY LYS PRO LEU ARG ASP LEU SER THR GLN SEQRES 23 A 367 THR ILE ARG GLU MET TYR ALA LEU THR GLN GLY ARG VAL SEQRES 24 A 367 PRO ILE ILE GLY VAL GLY GLY VAL SER SER GLY GLN ASP SEQRES 25 A 367 ALA LEU GLU LYS ILE ARG ALA GLY ALA SER LEU VAL GLN SEQRES 26 A 367 LEU TYR THR ALA LEU THR PHE TRP GLY PRO PRO VAL VAL SEQRES 27 A 367 GLY LYS VAL LYS ARG GLU LEU GLU ALA LEU LEU LYS GLU SEQRES 28 A 367 GLN GLY PHE GLY GLY VAL THR ASP ALA ILE GLY ALA ASP SEQRES 29 A 367 HIS ARG ARG HET SO4 A 401 5 HET ACT A 402 4 HET ACT A 403 4 HET FMN A 398 31 HET ORO A 399 11 HET R2C A 400 25 HET DDQ A 700 14 HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM ORO OROTIC ACID HETNAM R2C 5-METHOXY-2-[(4-PHENOXYPHENYL)AMINO]BENZOIC ACID HETNAM DDQ DECYLAMINE-N,N-DIMETHYL-N-OXIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 SO4 O4 S 2- FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 5 FMN C17 H21 N4 O9 P FORMUL 6 ORO C5 H4 N2 O4 FORMUL 7 R2C C20 H17 N O4 FORMUL 8 DDQ C12 H27 N O FORMUL 9 HOH *231(H2 O) HELIX 1 1 ASP A 34 HIS A 41 1 8 HELIX 2 2 HIS A 41 LEU A 50 1 10 HELIX 3 3 ASP A 51 GLY A 66 1 16 HELIX 4 4 SER A 76 GLU A 80 5 5 HELIX 5 5 ALA A 104 MET A 111 1 8 HELIX 6 6 PRO A 138 ASP A 140 5 3 HELIX 7 7 GLY A 153 ALA A 163 1 11 HELIX 8 8 ARG A 164 ASP A 174 1 11 HELIX 9 9 ASP A 190 GLY A 203 1 14 HELIX 10 10 PRO A 204 ALA A 206 5 3 HELIX 11 11 GLY A 220 GLN A 225 5 6 HELIX 12 12 GLY A 226 GLY A 243 1 18 HELIX 13 13 ARG A 245 ARG A 249 5 5 HELIX 14 14 THR A 261 GLY A 276 1 16 HELIX 15 15 LEU A 309 THR A 324 1 16 HELIX 16 16 SER A 338 GLY A 349 1 12 HELIX 17 17 TYR A 356 GLY A 363 1 8 HELIX 18 18 PRO A 365 GLN A 381 1 17 HELIX 19 19 GLY A 385 ILE A 390 1 6 HELIX 20 20 GLY A 391 ARG A 396 5 6 SHEET 1 A 2 VAL A 81 VAL A 83 0 SHEET 2 A 2 HIS A 86 PHE A 88 -1 O PHE A 88 N VAL A 81 SHEET 1 B 9 VAL A 92 ILE A 94 0 SHEET 2 B 9 PHE A 115 VAL A 121 1 O PHE A 115 N ILE A 94 SHEET 3 B 9 LEU A 178 LEU A 182 1 O GLY A 179 N VAL A 116 SHEET 4 B 9 TYR A 208 ASN A 212 1 O VAL A 210 N LEU A 182 SHEET 5 B 9 ALA A 251 ILE A 256 1 O LEU A 253 N VAL A 211 SHEET 6 B 9 GLY A 279 VAL A 282 1 O ILE A 281 N ILE A 256 SHEET 7 B 9 ILE A 330 VAL A 333 1 O ILE A 331 N LEU A 280 SHEET 8 B 9 LEU A 352 LEU A 355 1 O LEU A 352 N GLY A 332 SHEET 9 B 9 VAL A 92 ILE A 94 1 N GLY A 93 O VAL A 353 SHEET 1 C 3 VAL A 134 LEU A 137 0 SHEET 2 C 3 ALA A 142 ASN A 145 -1 O ALA A 142 N LEU A 137 SHEET 3 C 3 GLY A 303 GLY A 306 -1 O SER A 305 N VAL A 143 CISPEP 1 THR A 32 GLY A 33 0 5.69 CISPEP 2 GLY A 119 SER A 120 0 2.83 CISPEP 3 ARG A 131 PRO A 132 0 -0.35 CISPEP 4 VAL A 282 THR A 283 0 9.85 SITE 1 AC1 2 ARG A 245 HIS A 248 SITE 1 AC2 7 LYS A 307 PRO A 308 ASP A 311 THR A 314 SITE 2 AC2 7 GLN A 315 ARG A 318 HOH A 725 SITE 1 AC3 3 GLU A 53 ASN A 150 HOH A 864 SITE 1 AC4 24 ALA A 95 ALA A 96 GLY A 97 LYS A 100 SITE 2 AC4 24 GLY A 119 SER A 120 ASN A 145 TYR A 147 SITE 3 AC4 24 ASN A 181 ASN A 212 LYS A 255 THR A 283 SITE 4 AC4 24 ASN A 284 THR A 285 SER A 305 GLY A 306 SITE 5 AC4 24 LEU A 309 GLY A 334 GLY A 335 LEU A 355 SITE 6 AC4 24 TYR A 356 THR A 357 HOH A 704 HOH A 730 SITE 1 AC5 10 LYS A 100 ASN A 145 TYR A 147 GLY A 148 SITE 2 AC5 10 PHE A 149 ASN A 212 SER A 215 ASN A 217 SITE 3 AC5 10 ASN A 284 THR A 285 SITE 1 AC6 15 TYR A 38 LEU A 42 MET A 43 LEU A 46 SITE 2 AC6 15 GLN A 47 PRO A 52 ALA A 55 HIS A 56 SITE 3 AC6 15 ALA A 59 LEU A 67 ARG A 136 TYR A 356 SITE 4 AC6 15 THR A 360 PRO A 364 HOH A 747 SITE 1 AC7 5 ALA A 31 LEU A 46 PHE A 62 LEU A 67 SITE 2 AC7 5 LEU A 68 CRYST1 90.410 90.410 122.070 90.00 90.00 120.00 P 32 2 1 6 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 0.011061 0.006386 0.000000 0.00000 SCALE2 0.000000 0.012772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008192 0.00000