HEADER OXIDOREDUCTASE 02-AUG-10 3O8A TITLE CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM DIHYDROOROTATE TITLE 2 DEHYDROGENASE BOUND WITH NOVEL INHIBITOR GENZ667348 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE HOMOLOG, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 158-383, 414-569; COMPND 5 SYNONYM: DHODEHASE, DIHYDROOROTATE OXIDASE; COMPND 6 EC: 1.3.5.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 GENE: DIHYDROOROTATE DEHYDROGENASE, PFF0160C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS ALPHA BETA FOLD, DIHYDROOROTATE DEHYDROGENASE, OXIDOREDUCTASE, KEYWDS 2 PYRIMIDINE BIOSYNTHESIS, GENZ667348, FAD, FLAVOPROTEIN, KEYWDS 3 MITOCHONDRION INNER MEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR X.DENG,M.L.BOOKER,M.A.PHILLIPS REVDAT 4 21-FEB-24 3O8A 1 REMARK SEQADV REVDAT 3 23-AUG-17 3O8A 1 SOURCE REMARK REVDAT 2 12-JAN-11 3O8A 1 JRNL REVDAT 1 18-AUG-10 3O8A 0 JRNL AUTH M.L.BOOKER,C.M.BASTOS,M.L.KRAMER,R.H.BARKER,R.SKERLJ, JRNL AUTH 2 A.B.SIDHU,X.DENG,C.CELATKA,J.F.CORTESE,J.E.GUERRERO BRAVO, JRNL AUTH 3 K.N.CRESPO LLADO,A.E.SERRANO,I.ANGULO-BARTUREN, JRNL AUTH 4 M.B.JIMENEZ-DIAZ,S.VIERA,H.GARUTI,S.WITTLIN, JRNL AUTH 5 P.PAPASTOGIANNIDIS,J.W.LIN,C.J.JANSE,S.M.KHAN,M.DURAISINGH, JRNL AUTH 6 B.COLEMAN,E.J.GOLDSMITH,M.A.PHILLIPS,B.MUNOZ,D.F.WIRTH, JRNL AUTH 7 J.D.KLINGER,R.WIEGAND,E.SYBERTZ JRNL TITL NOVEL INHIBITORS OF PLASMODIUM FALCIPARUM DIHYDROOROTATE JRNL TITL 2 DEHYDROGENASE WITH ANTI-MALARIAL ACTIVITY IN THE MOUSE JRNL TITL 3 MODEL. JRNL REF J.BIOL.CHEM. V. 285 33054 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20702404 JRNL DOI 10.1074/JBC.M110.162081 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 24110 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1297 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1783 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2974 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.69000 REMARK 3 B22 (A**2) : 1.69000 REMARK 3 B33 (A**2) : -2.53000 REMARK 3 B12 (A**2) : 0.84000 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): 0.246 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.192 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.012 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3112 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4198 ; 1.581 ; 2.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 374 ; 5.965 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;39.398 ;25.540 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 574 ;15.170 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;18.233 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 465 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2290 ; 0.006 ; 0.021 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): 1858 ; 0.649 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3006 ; 1.230 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1254 ; 1.898 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1188 ; 3.075 ; 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 : 4 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 165 A 560 REMARK 3 ORIGIN FOR THE GROUP (A): 22.1402 -11.7059 0.5416 REMARK 3 T TENSOR REMARK 3 T11: 0.0419 T22: 0.1915 REMARK 3 T33: 0.0732 T12: -0.0519 REMARK 3 T13: 0.0430 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 2.4900 L22: 1.9829 REMARK 3 L33: 1.5387 L12: -0.1333 REMARK 3 L13: 0.0727 L23: 0.0207 REMARK 3 S TENSOR REMARK 3 S11: -0.2338 S12: 0.2421 S13: -0.3330 REMARK 3 S21: 0.0127 S22: 0.1825 S23: 0.0368 REMARK 3 S31: 0.1538 S32: -0.1730 S33: 0.0513 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 1001 A 1001 REMARK 3 ORIGIN FOR THE GROUP (A): 28.5970 -10.3309 16.9919 REMARK 3 T TENSOR REMARK 3 T11: 0.1181 T22: 0.1648 REMARK 3 T33: 0.1378 T12: 0.0456 REMARK 3 T13: 0.0718 T23: 0.0908 REMARK 3 L TENSOR REMARK 3 L11: 2.2144 L22: 12.5270 REMARK 3 L33: 6.2511 L12: 0.4822 REMARK 3 L13: 0.3820 L23: 8.8094 REMARK 3 S TENSOR REMARK 3 S11: -0.0539 S12: -0.1180 S13: -0.1745 REMARK 3 S21: 0.3039 S22: 0.3241 S23: -0.2661 REMARK 3 S31: 0.1483 S32: 0.1724 S33: -0.2702 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 1002 A 1002 REMARK 3 ORIGIN FOR THE GROUP (A): 18.8692 -14.8892 6.4168 REMARK 3 T TENSOR REMARK 3 T11: 0.1940 T22: 0.2326 REMARK 3 T33: 0.3146 T12: -0.0466 REMARK 3 T13: 0.0091 T23: 0.0570 REMARK 3 L TENSOR REMARK 3 L11: 0.5151 L22: 7.0975 REMARK 3 L33: 10.0691 L12: -1.4697 REMARK 3 L13: -2.1515 L23: 7.9108 REMARK 3 S TENSOR REMARK 3 S11: -0.2409 S12: 0.0684 S13: 0.0192 REMARK 3 S21: 0.3951 S22: -0.0889 S23: 0.6299 REMARK 3 S31: 0.8249 S32: -0.2344 S33: 0.3297 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 1003 A 1003 REMARK 3 ORIGIN FOR THE GROUP (A): 13.4834 -13.6093 7.3255 REMARK 3 T TENSOR REMARK 3 T11: 0.1201 T22: 0.1255 REMARK 3 T33: 0.0698 T12: -0.0641 REMARK 3 T13: 0.0370 T23: 0.0107 REMARK 3 L TENSOR REMARK 3 L11: 9.6441 L22: 3.8783 REMARK 3 L33: 15.9551 L12: 4.4893 REMARK 3 L13: -1.2351 L23: 4.7395 REMARK 3 S TENSOR REMARK 3 S11: -0.1397 S12: -0.0517 S13: 0.2671 REMARK 3 S21: -0.2780 S22: 0.0018 S23: 0.1897 REMARK 3 S31: -0.6557 S32: 0.1415 S33: 0.1379 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 3O8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060790. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97948 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK HIGH-RESOLUTION REMARK 200 DOUBLE-CRYSTAL MONOCHROMATOR 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 : 25502 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.75000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE, PH 4.3, 13-15% PEG4000, 25% GLYCEROL, AND 10 MM DTT, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,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 46.23967 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 92.47933 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 46.23967 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 92.47933 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: 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 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 MET A 125 REMARK 465 GLY A 126 REMARK 465 SER A 127 REMARK 465 SER A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 SER A 135 REMARK 465 SER A 136 REMARK 465 GLY A 137 REMARK 465 LEU A 138 REMARK 465 VAL A 139 REMARK 465 PRO A 140 REMARK 465 ARG A 141 REMARK 465 GLY A 142 REMARK 465 SER A 143 REMARK 465 HIS A 144 REMARK 465 MET A 145 REMARK 465 ALA A 146 REMARK 465 SER A 147 REMARK 465 MET A 148 REMARK 465 THR A 149 REMARK 465 GLY A 150 REMARK 465 GLY A 151 REMARK 465 GLN A 152 REMARK 465 GLN A 153 REMARK 465 GLY A 154 REMARK 465 ARG A 155 REMARK 465 ASP A 156 REMARK 465 PRO A 157 REMARK 465 PHE A 158 REMARK 465 GLU A 159 REMARK 465 SER A 160 REMARK 465 HIS A 566 REMARK 465 SER A 567 REMARK 465 LYS A 568 REMARK 465 SER A 569 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 CYS A 283 CB CYS A 283 SG -0.112 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 296 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 296 NE - CZ - NH2 ANGL. DEV. = -4.4 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 LYS A 213 -133.00 48.35 REMARK 500 ASP A 228 79.22 -112.52 REMARK 500 CYS A 233 58.74 -151.37 REMARK 500 PRO A 346 34.38 -97.92 REMARK 500 LEU A 351 -49.73 69.79 REMARK 500 ASN A 418 -157.38 -134.17 REMARK 500 TYR A 528 -67.08 -140.50 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 O8A A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ORO A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LDA A 1004 DBREF 3O8A A 158 383 UNP Q08210 PYRD_PLAF7 158 383 DBREF 3O8A A 414 569 UNP Q08210 PYRD_PLAF7 414 569 SEQADV 3O8A MET A 125 UNP Q08210 EXPRESSION TAG SEQADV 3O8A GLY A 126 UNP Q08210 EXPRESSION TAG SEQADV 3O8A SER A 127 UNP Q08210 EXPRESSION TAG SEQADV 3O8A SER A 128 UNP Q08210 EXPRESSION TAG SEQADV 3O8A HIS A 129 UNP Q08210 EXPRESSION TAG SEQADV 3O8A HIS A 130 UNP Q08210 EXPRESSION TAG SEQADV 3O8A HIS A 131 UNP Q08210 EXPRESSION TAG SEQADV 3O8A HIS A 132 UNP Q08210 EXPRESSION TAG SEQADV 3O8A HIS A 133 UNP Q08210 EXPRESSION TAG SEQADV 3O8A HIS A 134 UNP Q08210 EXPRESSION TAG SEQADV 3O8A SER A 135 UNP Q08210 EXPRESSION TAG SEQADV 3O8A SER A 136 UNP Q08210 EXPRESSION TAG SEQADV 3O8A GLY A 137 UNP Q08210 EXPRESSION TAG SEQADV 3O8A LEU A 138 UNP Q08210 EXPRESSION TAG SEQADV 3O8A VAL A 139 UNP Q08210 EXPRESSION TAG SEQADV 3O8A PRO A 140 UNP Q08210 EXPRESSION TAG SEQADV 3O8A ARG A 141 UNP Q08210 EXPRESSION TAG SEQADV 3O8A GLY A 142 UNP Q08210 EXPRESSION TAG SEQADV 3O8A SER A 143 UNP Q08210 EXPRESSION TAG SEQADV 3O8A HIS A 144 UNP Q08210 EXPRESSION TAG SEQADV 3O8A MET A 145 UNP Q08210 EXPRESSION TAG SEQADV 3O8A ALA A 146 UNP Q08210 EXPRESSION TAG SEQADV 3O8A SER A 147 UNP Q08210 EXPRESSION TAG SEQADV 3O8A MET A 148 UNP Q08210 EXPRESSION TAG SEQADV 3O8A THR A 149 UNP Q08210 EXPRESSION TAG SEQADV 3O8A GLY A 150 UNP Q08210 EXPRESSION TAG SEQADV 3O8A GLY A 151 UNP Q08210 EXPRESSION TAG SEQADV 3O8A GLN A 152 UNP Q08210 EXPRESSION TAG SEQADV 3O8A GLN A 153 UNP Q08210 EXPRESSION TAG SEQADV 3O8A GLY A 154 UNP Q08210 EXPRESSION TAG SEQADV 3O8A ARG A 155 UNP Q08210 EXPRESSION TAG SEQADV 3O8A ASP A 156 UNP Q08210 EXPRESSION TAG SEQADV 3O8A PRO A 157 UNP Q08210 EXPRESSION TAG SEQRES 1 A 415 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 415 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 415 GLY GLN GLN GLY ARG ASP PRO PHE GLU SER TYR ASN PRO SEQRES 4 A 415 GLU PHE PHE LEU TYR ASP ILE PHE LEU LYS PHE CYS LEU SEQRES 5 A 415 LYS TYR ILE ASP GLY GLU ILE CYS HIS ASP LEU PHE LEU SEQRES 6 A 415 LEU LEU GLY LYS TYR ASN ILE LEU PRO TYR ASP THR SER SEQRES 7 A 415 ASN ASP SER ILE TYR ALA CYS THR ASN ILE LYS HIS LEU SEQRES 8 A 415 ASP PHE ILE ASN PRO PHE GLY VAL ALA ALA GLY PHE ASP SEQRES 9 A 415 LYS ASN GLY VAL CYS ILE ASP SER ILE LEU LYS LEU GLY SEQRES 10 A 415 PHE SER PHE ILE GLU ILE GLY THR ILE THR PRO ARG GLY SEQRES 11 A 415 GLN THR GLY ASN ALA LYS PRO ARG ILE PHE ARG ASP VAL SEQRES 12 A 415 GLU SER ARG SER ILE ILE ASN SER CYS GLY PHE ASN ASN SEQRES 13 A 415 MET GLY CYS ASP LYS VAL THR GLU ASN LEU ILE LEU PHE SEQRES 14 A 415 ARG LYS ARG GLN GLU GLU ASP LYS LEU LEU SER LYS HIS SEQRES 15 A 415 ILE VAL GLY VAL SER ILE GLY LYS ASN LYS ASP THR VAL SEQRES 16 A 415 ASN ILE VAL ASP ASP LEU LYS TYR CYS ILE ASN LYS ILE SEQRES 17 A 415 GLY ARG TYR ALA ASP TYR ILE ALA ILE ASN VAL SER SER SEQRES 18 A 415 PRO ASN THR PRO GLY LEU ARG ASP ASN GLN GLU ALA GLY SEQRES 19 A 415 LYS LEU LYS ASN ILE ILE LEU SER VAL LYS GLU GLU ILE SEQRES 20 A 415 ASP ASN LEU GLU LYS ASN ASN ILE MET ASN ASP GLU PHE SEQRES 21 A 415 LEU TRP PHE ASN THR THR LYS LYS LYS PRO LEU VAL PHE SEQRES 22 A 415 VAL LYS LEU ALA PRO ASP LEU ASN GLN GLU GLN LYS LYS SEQRES 23 A 415 GLU ILE ALA ASP VAL LEU LEU GLU THR ASN ILE ASP GLY SEQRES 24 A 415 MET ILE ILE SER ASN THR THR THR GLN ILE ASN ASP ILE SEQRES 25 A 415 LYS SER PHE GLU ASN LYS LYS GLY GLY VAL SER GLY ALA SEQRES 26 A 415 LYS LEU LYS ASP ILE SER THR LYS PHE ILE CYS GLU MET SEQRES 27 A 415 TYR ASN TYR THR ASN LYS GLN ILE PRO ILE ILE ALA SER SEQRES 28 A 415 GLY GLY ILE PHE SER GLY LEU ASP ALA LEU GLU LYS ILE SEQRES 29 A 415 GLU ALA GLY ALA SER VAL CYS GLN LEU TYR SER CYS LEU SEQRES 30 A 415 VAL PHE ASN GLY MET LYS SER ALA VAL GLN ILE LYS ARG SEQRES 31 A 415 GLU LEU ASN HIS LEU LEU TYR GLN ARG GLY TYR TYR ASN SEQRES 32 A 415 LEU LYS GLU ALA ILE GLY ARG LYS HIS SER LYS SER HET O8A A1001 26 HET FMN A1002 31 HET ORO A1003 11 HET LDA A1004 16 HETNAM O8A N-CYCLOPROPYL-5-[2-METHYL-5-(TRIFLUOROMETHOXY)-1H- HETNAM 2 O8A BENZIMIDAZOL-1-YL]THIOPHENE-2-CARBOXAMIDE HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM ORO OROTIC ACID HETNAM LDA LAURYL DIMETHYLAMINE-N-OXIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 O8A C17 H14 F3 N3 O2 S FORMUL 3 FMN C17 H21 N4 O9 P FORMUL 4 ORO C5 H4 N2 O4 FORMUL 5 LDA C14 H31 N O FORMUL 6 HOH *36(H2 O) HELIX 1 1 ASN A 162 ILE A 179 1 18 HELIX 2 2 ASP A 180 TYR A 194 1 15 HELIX 3 3 CYS A 233 LYS A 239 1 7 HELIX 4 4 GLY A 282 ASP A 300 1 19 HELIX 5 5 ASN A 320 GLY A 333 1 14 HELIX 6 6 ARG A 334 ALA A 336 5 3 HELIX 7 7 LEU A 351 GLN A 355 5 5 HELIX 8 8 GLU A 356 ASN A 378 1 23 HELIX 9 9 ASN A 381 TRP A 416 1 6 HELIX 10 10 ASN A 435 ASN A 450 1 16 HELIX 11 11 ILE A 466 GLU A 470 5 5 HELIX 12 12 LEU A 481 THR A 496 1 16 HELIX 13 13 SER A 510 GLY A 521 1 12 HELIX 14 14 TYR A 528 GLY A 535 1 8 HELIX 15 15 LYS A 537 ARG A 553 1 17 HELIX 16 16 LEU A 558 ILE A 562 5 5 SHEET 1 A 2 THR A 210 ILE A 212 0 SHEET 2 A 2 LEU A 215 PHE A 217 -1 O PHE A 217 N THR A 210 SHEET 1 B 9 PHE A 221 VAL A 223 0 SHEET 2 B 9 PHE A 244 ILE A 250 1 O GLU A 246 N VAL A 223 SHEET 3 B 9 ILE A 307 ILE A 312 1 O SER A 311 N ILE A 247 SHEET 4 B 9 TYR A 338 ASN A 342 1 O ALA A 340 N ILE A 312 SHEET 5 B 9 LEU A 425 LEU A 430 1 O PHE A 427 N ILE A 341 SHEET 6 B 9 GLY A 453 ILE A 456 1 O ILE A 455 N VAL A 428 SHEET 7 B 9 ILE A 502 ALA A 504 1 O ILE A 503 N MET A 454 SHEET 8 B 9 ALA A 522 LEU A 527 1 O SER A 523 N ILE A 502 SHEET 9 B 9 PHE A 221 VAL A 223 1 N GLY A 222 O LEU A 527 SHEET 1 C 3 ILE A 263 ASP A 266 0 SHEET 2 C 3 SER A 271 ASN A 274 -1 O SER A 271 N ASP A 266 SHEET 3 C 3 GLY A 475 GLY A 478 -1 O SER A 477 N ILE A 272 CISPEP 1 GLY A 248 THR A 249 0 7.51 CISPEP 2 LYS A 260 PRO A 261 0 -2.44 CISPEP 3 PRO A 349 GLY A 350 0 -11.03 CISPEP 4 ILE A 456 SER A 457 0 6.03 CISPEP 5 SER A 505 GLY A 506 0 -11.26 SITE 1 AC1 15 TYR A 168 PHE A 171 LEU A 172 CYS A 175 SITE 2 AC1 15 GLY A 181 CYS A 184 HIS A 185 LEU A 187 SITE 3 AC1 15 PHE A 188 LEU A 191 ILE A 263 ARG A 265 SITE 4 AC1 15 LEU A 531 VAL A 532 MET A 536 SITE 1 AC2 20 ALA A 224 ALA A 225 GLY A 226 LYS A 229 SITE 2 AC2 20 THR A 249 ASN A 274 ASN A 342 LYS A 429 SITE 3 AC2 20 SER A 457 ASN A 458 SER A 477 GLY A 478 SITE 4 AC2 20 SER A 505 GLY A 506 GLY A 507 TYR A 528 SITE 5 AC2 20 SER A 529 HOH A 604 HOH A 628 ORO A1003 SITE 1 AC3 11 LYS A 229 ASN A 274 CYS A 276 GLY A 277 SITE 2 AC3 11 PHE A 278 ASN A 342 SER A 345 ASN A 347 SITE 3 AC3 11 ASN A 458 THR A 459 FMN A1002 SITE 1 AC4 6 GLU A 164 TYR A 168 ASN A 195 ILE A 196 SITE 2 AC4 6 LEU A 197 TYR A 199 CRYST1 85.287 85.287 138.719 90.00 90.00 120.00 P 64 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 0.011725 0.006769 0.000000 0.00000 SCALE2 0.000000 0.013539 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007209 0.00000