HEADER OXIDOREDUCTASE 27-MAR-00 1EP3 TITLE CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE TITLE 2 B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT); COMPND 3 CHAIN: A; COMPND 4 EC: 1.3.3.1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT); COMPND 8 CHAIN: B; COMPND 9 EC: 1.3.3.1; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS; SOURCE 3 ORGANISM_TAXID: 1358; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS; SOURCE 8 ORGANISM_TAXID: 1358; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HETEROTETRAMER, ALPHA-BETA BARREL, BETA SANDWICH, FAD DOMAIN, KEYWDS 2 ALPHA/BETA NADP DOMAIN, FES CLUSTER BINDING DOMAIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.ROWLAND,S.NORAGER,K.F.JENSEN,S.LARSEN REVDAT 4 09-AUG-23 1EP3 1 REMARK SEQADV SHEET REVDAT 3 13-JUL-11 1EP3 1 VERSN REVDAT 2 24-FEB-09 1EP3 1 VERSN REVDAT 1 17-JAN-01 1EP3 0 JRNL AUTH P.ROWLAND,S.NORAGER,K.F.JENSEN,S.LARSEN JRNL TITL STRUCTURE OF DIHYDROOROTATE DEHYDROGENASE B: ELECTRON JRNL TITL 2 TRANSFER BETWEEN TWO FLAVIN GROUPS BRIDGED BY AN JRNL TITL 3 IRON-SULPHUR CLUSTER. JRNL REF STRUCTURE FOLD.DES. V. 8 1227 2000 JRNL REFN ISSN 0969-2126 JRNL PMID 11188687 JRNL DOI 10.1016/S0969-2126(00)00530-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.ROWLAND,F.S.NIELSEN,K.F.JENSEN,S.LARSEN REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF THE HETEROTETRAMERIC DIHYDROOROTATE DEHYDROGENASE B OF REMARK 1 TITL 3 LACTOCOCCUS LACTIS, A FLAVOPROTEIN ENZYME SYSTEM CONSISTING REMARK 1 TITL 4 OF TWO PYRDB SUBUNITS AND TWO IRON-SULFUR CLUSTER CONTAINING REMARK 1 TITL 5 PYRK SUBUNITS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 53 802 1997 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444997006203 REMARK 1 REFERENCE 2 REMARK 1 AUTH F.S.NIELSEN,P.S.ANDERSEN,K.F.JENSEN REMARK 1 TITL THE B FORM OF DIHYDROOROTATE DEHYDROGENASE FROM LACTOCOCCUS REMARK 1 TITL 2 LACTIS CONSISTS OF TWO DIFFERENT SUBUNITS, ENCODED BY THE REMARK 1 TITL 3 PYRDB AND PYRK GENES, AND CONTAINS FMN, FAD AND [FES] REDOX REMARK 1 TITL 4 CENTERS REMARK 1 REF J.BIOL.CHEM. V. 271 29359 1996 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.271.46.29359 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.F.JENSEN,O.BJORNBERG,F.S.NIELSEN,M.OTTOSEN,P.G.SORENSEN, REMARK 1 AUTH 2 P.ROWLAND,S.NORAGER,S.LARSEN REMARK 1 TITL ROLES OF THREE PROSTHETIC GROUPS IN TETRAMERIC REMARK 1 TITL 2 DIHYDROOROTATE DEHYDROGENASE B FROM LACTOCOCCUS LACTIS REMARK 1 REF FLAVINS AND FLAVOPROTEINS V.13TH 599 1999 REMARK 1 PUBL BERLIN, GERMANY: RUDOLF WEBER, DR. -ING., AGENCY FOR REMARK 1 PUBL 2 SCIENTIFIC PUBLICATIONS REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 35305 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3509 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5106 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 584 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4300 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 466 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.426 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.139 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 79.13 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EP3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000010787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.84690 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35821 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.6200 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) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ID 1EP1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1 - 2.4 M AMMONIUM SULFATE, 0.1 M NA REMARK 280 -ACETATE PH 4 TO 5, PH 4.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 99.94500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.70327 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 26.75667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 99.94500 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 57.70327 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 26.75667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 99.94500 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 57.70327 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 26.75667 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 99.94500 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 57.70327 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 26.75667 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 99.94500 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 57.70327 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 26.75667 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 99.94500 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 57.70327 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 26.75667 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 115.40655 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 53.51333 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 115.40655 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 53.51333 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 115.40655 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 53.51333 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 115.40655 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 53.51333 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 115.40655 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 53.51333 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 115.40655 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 53.51333 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 13990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 346.21964 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 80.27000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 578 LIES ON A SPECIAL POSITION. 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 B 1 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 GLY B 257 N GLY B 257 CA 0.095 REMARK 500 LEU B 262 C LEU B 262 OXT 0.238 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 GLN B 259 C - N - CA ANGL. DEV. = -16.4 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 SER A 44 -175.77 -176.43 REMARK 500 ILE A 216 -67.14 72.41 REMARK 500 LYS A 310 90.36 -44.20 REMARK 500 TYR B 18 109.39 -55.85 REMARK 500 ASP B 34 -59.55 -162.94 REMARK 500 LYS B 65 36.90 71.85 REMARK 500 GLU B 106 47.71 -81.95 REMARK 500 SER B 109 -3.11 -52.65 REMARK 500 ASN B 159 30.33 -77.87 REMARK 500 ASN B 162 39.48 36.17 REMARK 500 TYR B 174 144.15 -175.82 REMARK 500 PHE B 189 159.81 173.48 REMARK 500 TYR B 210 50.96 -110.38 REMARK 500 ALA B 225 -83.65 -133.50 REMARK 500 CYS B 234 30.77 -87.93 REMARK 500 LYS B 258 -107.57 -59.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES B 503 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 226 SG REMARK 620 2 FES B 503 S1 106.9 REMARK 620 3 FES B 503 S2 107.6 100.5 REMARK 620 4 CYS B 231 SG 104.6 116.5 120.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES B 503 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 234 SG REMARK 620 2 FES B 503 S1 127.5 REMARK 620 3 FES B 503 S2 110.8 102.8 REMARK 620 4 CYS B 249 SG 103.0 109.2 100.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES B 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EP1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE REMARK 900 DEHYDROGENASE B AT 277.15 K. REMARK 900 RELATED ID: 1EP2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE REMARK 900 DEHYDROGENASE B - COMPLEX WITH OROTATE. DBREF 1EP3 A 1 311 UNP P54322 PYRDB_LACLC 1 311 DBREF 1EP3 B 1 262 UNP P56968 PYRK_LACLC 1 262 SEQADV 1EP3 ALA A 123 UNP P54322 ARG 123 CONFLICT SEQADV 1EP3 ASP A 255 UNP P54322 VAL 255 CONFLICT SEQADV 1EP3 ALA A 266 UNP P54322 ARG 266 CONFLICT SEQRES 1 A 311 MET THR GLU ASN ASN ARG LEU SER VAL LYS LEU PRO GLY SEQRES 2 A 311 LEU ASP LEU LYS ASN PRO ILE ILE PRO ALA SER GLY CYS SEQRES 3 A 311 PHE GLY PHE GLY GLU GLU TYR ALA LYS TYR TYR ASP LEU SEQRES 4 A 311 ASN LYS LEU GLY SER ILE MET VAL LYS ALA THR THR LEU SEQRES 5 A 311 HIS PRO ARG PHE GLY ASN PRO THR PRO ARG VAL ALA GLU SEQRES 6 A 311 THR ALA SER GLY MET LEU ASN ALA ILE GLY LEU GLN ASN SEQRES 7 A 311 PRO GLY LEU GLU VAL ILE MET THR GLU LYS LEU PRO TRP SEQRES 8 A 311 LEU ASN GLU ASN PHE PRO GLU LEU PRO ILE ILE ALA ASN SEQRES 9 A 311 VAL ALA GLY SER GLU GLU ALA ASP TYR VAL ALA VAL CYS SEQRES 10 A 311 ALA LYS ILE GLY ASP ALA ALA ASN VAL LYS ALA ILE GLU SEQRES 11 A 311 LEU ASN ILE SER CYS PRO ASN VAL LYS HIS GLY GLY GLN SEQRES 12 A 311 ALA PHE GLY THR ASP PRO GLU VAL ALA ALA ALA LEU VAL SEQRES 13 A 311 LYS ALA CYS LYS ALA VAL SER LYS VAL PRO LEU TYR VAL SEQRES 14 A 311 LYS LEU SER PRO ASN VAL THR ASP ILE VAL PRO ILE ALA SEQRES 15 A 311 LYS ALA VAL GLU ALA ALA GLY ALA ASP GLY LEU THR MET SEQRES 16 A 311 ILE ASN THR LEU MET GLY VAL ARG PHE ASP LEU LYS THR SEQRES 17 A 311 ARG GLN PRO ILE LEU ALA ASN ILE THR GLY GLY LEU SER SEQRES 18 A 311 GLY PRO ALA ILE LYS PRO VAL ALA LEU LYS LEU ILE HIS SEQRES 19 A 311 GLN VAL ALA GLN ASP VAL ASP ILE PRO ILE ILE GLY MET SEQRES 20 A 311 GLY GLY VAL ALA ASN ALA GLN ASP VAL LEU GLU MET TYR SEQRES 21 A 311 MET ALA GLY ALA SER ALA VAL ALA VAL GLY THR ALA ASN SEQRES 22 A 311 PHE ALA ASP PRO PHE VAL CYS PRO LYS ILE ILE ASP LYS SEQRES 23 A 311 LEU PRO GLU LEU MET ASP GLN TYR ARG ILE GLU SER LEU SEQRES 24 A 311 GLU SER LEU ILE GLN GLU VAL LYS GLU GLY LYS LYS SEQRES 1 B 262 MET SER GLN LEU GLN GLU MET MET THR VAL VAL SER GLN SEQRES 2 B 262 ARG GLU VAL ALA TYR ASN ILE PHE GLU MET VAL LEU LYS SEQRES 3 B 262 GLY THR LEU VAL ASP GLU MET ASP LEU PRO GLY GLN PHE SEQRES 4 B 262 LEU HIS LEU ALA VAL PRO ASN GLY ALA MET LEU LEU ARG SEQRES 5 B 262 ARG PRO ILE SER ILE SER SER TRP ASP LYS ARG ALA LYS SEQRES 6 B 262 THR CYS THR ILE LEU TYR ARG ILE GLY ASP GLU THR THR SEQRES 7 B 262 GLY THR TYR LYS LEU SER LYS LEU GLU SER GLY ALA LYS SEQRES 8 B 262 VAL ASP VAL MET GLY PRO LEU GLY ASN GLY PHE PRO VAL SEQRES 9 B 262 ALA GLU VAL THR SER THR ASP LYS ILE LEU ILE ILE GLY SEQRES 10 B 262 GLY GLY ILE GLY VAL PRO PRO LEU TYR GLU LEU ALA LYS SEQRES 11 B 262 GLN LEU GLU LYS THR GLY CYS GLN MET THR ILE LEU LEU SEQRES 12 B 262 GLY PHE ALA SER GLU ASN VAL LYS ILE LEU GLU ASN GLU SEQRES 13 B 262 PHE SER ASN LEU LYS ASN VAL THR LEU LYS ILE ALA THR SEQRES 14 B 262 ASP ASP GLY SER TYR GLY THR LYS GLY HIS VAL GLY MET SEQRES 15 B 262 LEU MET ASN GLU ILE ASP PHE GLU VAL ASP ALA LEU TYR SEQRES 16 B 262 THR CYS GLY ALA PRO ALA MET LEU LYS ALA VAL ALA LYS SEQRES 17 B 262 LYS TYR ASP GLN LEU GLU ARG LEU TYR ILE SER MET GLU SEQRES 18 B 262 SER ARG MET ALA CYS GLY ILE GLY ALA CYS TYR ALA CYS SEQRES 19 B 262 VAL GLU HIS ASP LYS GLU ASP GLU SER HIS ALA LEU LYS SEQRES 20 B 262 VAL CYS GLU ASP GLY PRO VAL PHE LEU GLY LYS GLN LEU SEQRES 21 B 262 SER LEU HET FMN A 501 31 HET FAD B 502 53 HET FES B 503 4 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FMN C17 H21 N4 O9 P FORMUL 4 FAD C27 H33 N9 O15 P2 FORMUL 5 FES FE2 S2 FORMUL 6 HOH *466(H2 O) HELIX 1 1 GLU A 32 TYR A 36 5 5 HELIX 2 2 ASP A 38 LEU A 42 5 5 HELIX 3 3 GLY A 80 GLU A 87 1 8 HELIX 4 4 GLU A 87 PHE A 96 1 10 HELIX 5 5 GLU A 109 GLY A 121 1 13 HELIX 6 6 ASN A 137 GLY A 141 5 5 HELIX 7 7 PHE A 145 THR A 147 5 3 HELIX 8 8 ASP A 148 SER A 163 1 16 HELIX 9 9 ILE A 178 ALA A 188 1 11 HELIX 10 10 GLY A 222 ALA A 224 5 3 HELIX 11 11 ILE A 225 GLN A 238 1 14 HELIX 12 12 ASN A 252 GLY A 263 1 12 HELIX 13 13 THR A 271 ASP A 276 1 6 HELIX 14 14 PHE A 278 TYR A 294 1 17 HELIX 15 15 SER A 298 GLY A 309 1 12 HELIX 16 16 THR B 28 MET B 33 5 6 HELIX 17 17 THR B 78 LYS B 85 1 8 HELIX 18 18 VAL B 122 THR B 135 1 14 HELIX 19 19 SER B 147 LYS B 151 5 5 HELIX 20 20 LEU B 153 ASN B 159 1 7 HELIX 21 21 HIS B 179 ILE B 187 1 9 HELIX 22 22 ALA B 199 TYR B 210 1 12 SHEET 1 A 2 VAL A 9 LEU A 11 0 SHEET 2 A 2 LEU A 14 LEU A 16 -1 O LEU A 14 N LEU A 11 SHEET 1 B 7 ILE A 20 PRO A 22 0 SHEET 2 B 7 ILE A 244 GLY A 246 0 SHEET 3 B 7 GLY A 192 MET A 195 1 O LEU A 193 N ILE A 245 SHEET 4 B 7 LEU A 167 LEU A 171 1 O LEU A 167 N GLY A 192 SHEET 5 B 7 VAL A 126 ASN A 132 1 O ILE A 129 N TYR A 168 SHEET 6 B 7 ILE A 101 VAL A 105 1 O ILE A 101 N LYS A 127 SHEET 7 B 7 ILE A 45 THR A 50 1 O ILE A 45 N ILE A 102 SHEET 1 C 4 VAL A 63 THR A 66 0 SHEET 2 C 4 GLY A 69 ASN A 72 -1 O GLY A 69 N THR A 66 SHEET 3 C 4 GLY A 218 SER A 221 -1 N GLY A 219 O ASN A 72 SHEET 4 C 4 LEU A 199 GLY A 201 -1 O LEU A 199 N LEU A 220 SHEET 1 D 7 ARG B 53 SER B 56 0 SHEET 2 D 7 PHE B 39 LEU B 42 -1 O LEU B 40 N ILE B 55 SHEET 3 D 7 LYS B 91 LEU B 98 -1 O MET B 95 N HIS B 41 SHEET 4 D 7 GLN B 5 ALA B 17 -1 O GLU B 6 N VAL B 94 SHEET 5 D 7 ILE B 20 LYS B 26 -1 N ILE B 20 O ALA B 17 SHEET 6 D 7 THR B 66 ARG B 72 -1 O CYS B 67 N LEU B 25 SHEET 7 D 7 SER B 59 ASP B 61 -1 O SER B 59 N THR B 68 SHEET 1 E 7 THR B 176 LYS B 177 0 SHEET 2 E 7 VAL B 163 THR B 169 1 O ILE B 167 N THR B 176 SHEET 3 E 7 GLN B 138 PHE B 145 1 O MET B 139 N THR B 164 SHEET 4 E 7 LYS B 112 GLY B 118 1 N ILE B 113 O GLN B 138 SHEET 5 E 7 ALA B 193 CYS B 197 1 O ALA B 193 N LEU B 114 SHEET 6 E 7 LEU B 216 SER B 219 1 O TYR B 217 N THR B 196 SHEET 7 E 7 VAL B 254 PHE B 255 -1 N PHE B 255 O ILE B 218 SHEET 1 F 2 VAL B 235 ASP B 238 0 SHEET 2 F 2 ASP B 241 LYS B 247 -1 N ASP B 241 O ASP B 238 LINK SG CYS B 226 FE1 FES B 503 1555 1555 2.32 LINK SG CYS B 231 FE1 FES B 503 1555 1555 2.32 LINK SG CYS B 234 FE2 FES B 503 1555 1555 2.10 LINK SG CYS B 249 FE2 FES B 503 1555 1555 2.33 CISPEP 1 THR A 60 PRO A 61 0 -0.30 CISPEP 2 MET A 195 ILE A 196 0 2.60 CISPEP 3 GLY B 96 PRO B 97 0 0.08 CISPEP 4 GLY B 252 PRO B 253 0 1.26 SITE 1 AC1 22 ALA A 23 SER A 24 GLY A 25 ALA A 49 SITE 2 AC1 22 ASN A 72 LEU A 76 ASN A 104 ASN A 132 SITE 3 AC1 22 LYS A 170 ILE A 196 ASN A 197 THR A 198 SITE 4 AC1 22 SER A 221 GLY A 222 MET A 247 GLY A 248 SITE 5 AC1 22 GLY A 249 GLY A 270 THR A 271 HOH A 505 SITE 6 AC1 22 HOH A 520 HOH A 549 SITE 1 AC2 24 LEU B 51 ARG B 53 PRO B 54 ILE B 55 SITE 2 AC2 24 SER B 56 LEU B 70 TYR B 71 ARG B 72 SITE 3 AC2 24 THR B 78 GLY B 79 THR B 80 ILE B 120 SITE 4 AC2 24 GLU B 221 SER B 222 ARG B 223 HOH B 508 SITE 5 AC2 24 HOH B 510 HOH B 511 HOH B 516 HOH B 530 SITE 6 AC2 24 HOH B 534 HOH B 538 HOH B 555 HOH B 596 SITE 1 AC3 9 MET B 224 ALA B 225 CYS B 226 GLY B 227 SITE 2 AC3 9 GLY B 229 CYS B 231 TYR B 232 CYS B 234 SITE 3 AC3 9 CYS B 249 CRYST1 199.890 199.890 80.270 90.00 90.00 120.00 H 3 2 18 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 0.005000 0.002890 0.000000 0.00000 SCALE2 0.000000 0.005780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012460 0.00000