HEADER OXIDOREDUCTASE 13-AUG-01 1JRB TITLE THE P56A MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE A COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE A; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.3.3.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 EXPRESSION_SYSTEM_STRAIN: SO6645; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PUHE23 KEYWDS HOMODIMER, ALPHA-BETA BARREL, FLAVOPROTEIN, OROTATE COMPLEX, MUTANT KEYWDS 2 ENZYME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.NORAGER,S.ARENT,O.BJORNBERG,M.OTTOSEN,L.LO LEGGIO,K.F.JENSEN, AUTHOR 2 S.LARSEN REVDAT 5 25-OCT-23 1JRB 1 REMARK REVDAT 4 10-NOV-21 1JRB 1 REMARK SEQADV REVDAT 3 23-MAY-18 1JRB 1 REMARK REVDAT 2 24-FEB-09 1JRB 1 VERSN REVDAT 1 09-SEP-03 1JRB 0 JRNL AUTH S.NORAGER,S.ARENT,O.BJORNBERG,M.OTTOSEN,L.LO LEGGIO, JRNL AUTH 2 K.F.JENSEN,S.LARSEN JRNL TITL LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE A MUTANTS JRNL TITL 2 REVEAL IMPORTANT FACETS OF THE ENZYMATIC FUNCTION JRNL REF J.BIOL.CHEM. V. 278 28812 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12732650 JRNL DOI 10.1074/JBC.M303767200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.BJORNBERG,P.ROWLAND,S.LARSEN,K.F.JENSEN REMARK 1 TITL ACTIVE SITE OF DIHYDROOROTATE DEHYDROGENASE A FROM REMARK 1 TITL 2 LACTOCOCCUS LACTIS INVESTIGATED BY CHEMICAL MODIFICATION AND REMARK 1 TITL 3 MUTAGENESIS REMARK 1 REF BIOCHEMISTRY V. 36 16197 1997 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI971628Y REMARK 1 REFERENCE 2 REMARK 1 AUTH P.ROWLAND,O.BJORNBERG,F.S.NIELSEN,K.F.JENSEN,S.LARSEN REMARK 1 TITL THE CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE REMARK 1 TITL 2 DEHYDROGENASE A COMPLEXED WITH THE ENZYME REACTION PRODUCT REMARK 1 TITL 3 THROWS LIGHT ON ITS ENZYMATIC FUNCTION REMARK 1 REF PROTEIN SCI. V. 7 1269 1998 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 3 REMARK 1 AUTH P.ROWLAND,F.S.NIELSEN,K.F.JENSEN,S.LARSEN REMARK 1 TITL THE CRYSTAL STRUCTURE OF THE FLAVIN CONTAINING ENZYME REMARK 1 TITL 2 DIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS REMARK 1 REF STRUCTURE V. 5 239 1997 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(97)00182-2 REMARK 1 REFERENCE 4 REMARK 1 AUTH F.S.NIELSEN,P.ROWLAND,S.LARSEN,K.F.JENSEN REMARK 1 TITL PURIFICATION AND CHARACTERISATION OF DIHYDROOROTATE REMARK 1 TITL 2 DEHYDROGENASE A FROM LACTOCOCCUS LACTIS, CRYSTALLISATION AND REMARK 1 TITL 3 PRELIMINARY X-RAY DIFFRACTION STUDIES OF THE ENZYME REMARK 1 REF PROTEIN SCI. V. 5 852 1996 REMARK 1 REFN ISSN 0961-8368 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 53904 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.069 REMARK 3 FREE R VALUE TEST SET COUNT : 5431 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4779 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 358 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.97 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.021 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.035 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.061 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.183 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.242 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.153 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 13.300; 7.000 REMARK 3 STAGGERED (DEGREES) : 13.000; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 27.000; 20.000 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 OTHER REFINEMENT REMARKS: DATA OBTAINED AFTER THE TERMINATION OF REMARK 3 THIS STRUCTURE HAS ENABLED US TO IDENTIFIE TO MG-IONS IN THE REMARK 3 LACTOCOCCUS LACTIS DHODA. THESE ARE ALSO PRESENT IN THE P56A REMARK 3 MUTANT BUT HAVE BEEN REFINED AS WATER MOLECULES 11 AND 23. THE REMARK 3 CLOSE CONTACTS WITH WATER MOLECULES ARE DUE TO DISORDERD REMARK 3 RESIDUES REFINED WITH LOW OCCUPATION. REMARK 4 REMARK 4 1JRB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014099. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.992 REMARK 200 MONOCHROMATOR : SI(111) SINGLE CRYSTAL 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 : 57637 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.200 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: LACTOCOCCUS LACTIS DHODA, PDB ID 2DOR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6K, NA-ACETATE, TRIS-HCL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 54.41100 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 300 REMARK: THE ASSYMETRIC UNIT CONTAINS REMARK 300 THE BIOLOGICAL HOMODIMER. 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: 6980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 132 CB CG OD1 ND2 REMARK 470 VAL A 133 CB CG1 CG2 REMARK 470 PRO A 134 CB CG CD REMARK 470 LYS A 136 CB CG CD CE NZ REMARK 470 CYS B 130 CB SG REMARK 470 PRO B 131 CB CG CD REMARK 470 ASN B 132 CB CG OD1 ND2 REMARK 470 VAL B 133 CB CG1 CG2 REMARK 470 PRO B 134 CB CG CD REMARK 470 LYS B 136 CB CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN B 92 O HOH B 2475 0.40 REMARK 500 OE1 GLN A 92 O HOH A 1459 0.46 REMARK 500 CG ASN B 90 O HOH B 2459 0.81 REMARK 500 NE2 GLN A 92 O HOH A 1456 0.85 REMARK 500 OD1 ASN B 90 O HOH B 2459 0.91 REMARK 500 NE2 GLN B 92 O HOH B 2452 1.01 REMARK 500 CD GLN B 92 O HOH B 2475 1.15 REMARK 500 CD GLN A 92 O HOH A 1459 1.34 REMARK 500 ND2 ASN B 90 O HOH B 2459 1.53 REMARK 500 CD GLN A 92 O HOH A 1456 1.61 REMARK 500 CD GLN B 92 O HOH B 2452 1.66 REMARK 500 CB ASN B 90 O HOH B 2459 2.19 REMARK 500 CG GLN B 92 O HOH B 2475 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 40 CZ TYR A 40 CE2 -0.080 REMARK 500 SER A 194 CB SER A 194 OG -0.101 REMARK 500 SER B 194 CB SER B 194 OG -0.095 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 ASN A 17 OD1 - CG - ND2 ANGL. DEV. = -17.6 DEGREES REMARK 500 ASN A 17 CB - CG - OD1 ANGL. DEV. = 17.2 DEGREES REMARK 500 CYS A 23 O - C - N ANGL. DEV. = -10.1 DEGREES REMARK 500 ILE A 26 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 TYR A 40 CB - CG - CD2 ANGL. DEV. = 3.8 DEGREES REMARK 500 TYR A 40 CD1 - CG - CD2 ANGL. DEV. = -13.2 DEGREES REMARK 500 TYR A 40 CB - CG - CD1 ANGL. DEV. = 9.5 DEGREES REMARK 500 TYR A 40 CG - CD1 - CE1 ANGL. DEV. = 7.2 DEGREES REMARK 500 TYR A 40 CG - CD2 - CE2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TYR A 40 CE1 - CZ - CE2 ANGL. DEV. = -12.2 DEGREES REMARK 500 TYR A 40 CZ - CE2 - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 LEU A 55 O - C - N ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 TYR A 58 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TYR A 58 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 PHE A 97 CB - CG - CD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASN A 127 OD1 - CG - ND2 ANGL. DEV. = -17.7 DEGREES REMARK 500 PHE A 169 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP A 175 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 SER A 191 O - C - N ANGL. DEV. = -15.7 DEGREES REMARK 500 TYR A 223 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 233 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 238 NE - CZ - NH1 ANGL. DEV. = 8.3 DEGREES REMARK 500 ASP A 303 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASN B 17 OD1 - CG - ND2 ANGL. DEV. = -19.1 DEGREES REMARK 500 MET B 24 CG - SD - CE ANGL. DEV. = -10.2 DEGREES REMARK 500 ASP B 28 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 TYR B 40 CB - CG - CD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 TYR B 40 CD1 - CG - CD2 ANGL. DEV. = -13.2 DEGREES REMARK 500 TYR B 40 CB - CG - CD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 TYR B 40 CG - CD1 - CE1 ANGL. DEV. = 6.9 DEGREES REMARK 500 TYR B 40 CG - CD2 - CE2 ANGL. DEV. = 6.5 DEGREES REMARK 500 TYR B 40 CE1 - CZ - CE2 ANGL. DEV. = -12.6 DEGREES REMARK 500 TYR B 40 CZ - CE2 - CD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 LEU B 55 CB - CA - C ANGL. DEV. = -14.6 DEGREES REMARK 500 LEU B 55 CA - C - N ANGL. DEV. = 16.2 DEGREES REMARK 500 LEU B 55 O - C - N ANGL. DEV. = -15.6 DEGREES REMARK 500 TYR B 58 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TYR B 79 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASN B 127 OD1 - CG - ND2 ANGL. DEV. = -19.9 DEGREES REMARK 500 SER B 191 N - CA - CB ANGL. DEV. = 10.7 DEGREES REMARK 500 SER B 191 CA - C - N ANGL. DEV. = 19.9 DEGREES REMARK 500 SER B 191 O - C - N ANGL. DEV. = -15.2 DEGREES REMARK 500 LEU B 229 CA - C - O ANGL. DEV. = 14.4 DEGREES REMARK 500 LEU B 229 O - C - N ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG B 238 NE - CZ - NH1 ANGL. DEV. = 11.3 DEGREES REMARK 500 ARG B 238 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG B 284 NE - CZ - NH1 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 CYS A 23 29.18 -155.54 REMARK 500 ALA A 56 119.66 -37.70 REMARK 500 ALA A 91 114.08 -179.32 REMARK 500 GLN A 92 20.74 -179.05 REMARK 500 GLU A 93 70.54 12.22 REMARK 500 SER A 129 23.37 -142.37 REMARK 500 LYS A 136 102.87 173.18 REMARK 500 GLN A 138 128.69 -32.64 REMARK 500 GLU A 252 -33.33 -132.81 REMARK 500 CYS B 23 23.51 -159.29 REMARK 500 ALA B 91 117.39 -177.72 REMARK 500 GLN B 92 19.67 178.19 REMARK 500 GLU B 93 70.31 12.67 REMARK 500 SER B 129 20.59 -148.35 REMARK 500 LYS B 136 103.27 172.32 REMARK 500 GLN B 138 126.17 -33.97 REMARK 500 PHE B 304 -1.35 -143.63 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 LEU A 55 ALA A 56 -55.14 REMARK 500 GLU A 93 GLY A 94 -147.61 REMARK 500 CYS A 130 PRO A 131 -142.62 REMARK 500 SER A 191 VAL A 192 45.24 REMARK 500 LEU B 55 ALA B 56 38.92 REMARK 500 GLU B 93 GLY B 94 -148.66 REMARK 500 CYS B 130 PRO B 131 -149.58 REMARK 500 SER B 191 VAL B 192 43.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALA A 37 -10.89 REMARK 500 LEU A 55 -15.50 REMARK 500 GLY A 122 -10.94 REMARK 500 SER A 191 16.90 REMARK 500 LEU B 55 25.91 REMARK 500 SER B 191 22.92 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 FMN A 1312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ORO A 1313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 2312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ORO B 2313 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DOR RELATED DB: PDB REMARK 900 1DOR CONTAINS NATIVE LACTOCOCCUS LACTIS DIHYDROOROTATE REMARK 900 DEHYDROGENASE A REMARK 900 RELATED ID: 2DOR RELATED DB: PDB REMARK 900 2DOR CONTAINS NATIVE LACTOCOCCUS LACTIS DIHYDROOROTATE REMARK 900 DEHYDROGENASE A COMPLEXED WITH OROTATE REMARK 900 RELATED ID: 1JQV RELATED DB: PDB REMARK 900 1JQV CONTAINS K213E MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATE REMARK 900 DEHYDROGENASE A REMARK 900 RELATED ID: 1JQX RELATED DB: PDB REMARK 900 1JQX CONTAINS R57A MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATE REMARK 900 DEHYDROGENASE A REMARK 900 RELATED ID: 1JRC RELATED DB: PDB REMARK 900 1JRC CONTAINS N67A MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATE REMARK 900 DEHYDROGENASE A DBREF 1JRB A 1 311 UNP P54321 PYRDA_LACLC 1 311 DBREF 1JRB B 1 311 UNP P54321 PYRDA_LACLC 1 311 SEQADV 1JRB ALA A 56 UNP P54321 PRO 56 ENGINEERED MUTATION SEQADV 1JRB ALA B 56 UNP P54321 PRO 56 ENGINEERED MUTATION SEQRES 1 A 311 MET LEU ASN THR THR PHE ALA ASN ALA LYS PHE ALA ASN SEQRES 2 A 311 PRO PHE MET ASN ALA SER GLY VAL HIS CYS MET THR ILE SEQRES 3 A 311 GLU ASP LEU GLU GLU LEU LYS ALA SER GLN ALA GLY ALA SEQRES 4 A 311 TYR ILE THR LYS SER SER THR LEU GLU LYS ARG GLU GLY SEQRES 5 A 311 ASN PRO LEU ALA ARG TYR VAL ASP LEU GLU LEU GLY SER SEQRES 6 A 311 ILE ASN SER MET GLY LEU PRO ASN LEU GLY PHE ASP TYR SEQRES 7 A 311 TYR LEU ASP TYR VAL LEU LYS ASN GLN LYS GLU ASN ALA SEQRES 8 A 311 GLN GLU GLY PRO ILE PHE PHE SER ILE ALA GLY MET SER SEQRES 9 A 311 ALA ALA GLU ASN ILE ALA MET LEU LYS LYS ILE GLN GLU SEQRES 10 A 311 SER ASP PHE SER GLY ILE THR GLU LEU ASN LEU SER CYS SEQRES 11 A 311 PRO ASN VAL PRO GLY LYS PRO GLN LEU ALA TYR ASP PHE SEQRES 12 A 311 GLU ALA THR GLU LYS LEU LEU LYS GLU VAL PHE THR PHE SEQRES 13 A 311 PHE THR LYS PRO LEU GLY VAL LYS LEU PRO PRO TYR PHE SEQRES 14 A 311 ASP LEU VAL HIS PHE ASP ILE MET ALA GLU ILE LEU ASN SEQRES 15 A 311 GLN PHE PRO LEU THR TYR VAL ASN SER VAL ASN SER ILE SEQRES 16 A 311 GLY ASN GLY LEU PHE ILE ASP PRO GLU ALA GLU SER VAL SEQRES 17 A 311 VAL ILE LYS PRO LYS ASP GLY PHE GLY GLY ILE GLY GLY SEQRES 18 A 311 ALA TYR ILE LYS PRO THR ALA LEU ALA ASN VAL ARG ALA SEQRES 19 A 311 PHE TYR THR ARG LEU LYS PRO GLU ILE GLN ILE ILE GLY SEQRES 20 A 311 THR GLY GLY ILE GLU THR GLY GLN ASP ALA PHE GLU HIS SEQRES 21 A 311 LEU LEU CYS GLY ALA THR MET LEU GLN ILE GLY THR ALA SEQRES 22 A 311 LEU HIS LYS GLU GLY PRO ALA ILE PHE ASP ARG ILE ILE SEQRES 23 A 311 LYS GLU LEU GLU GLU ILE MET ASN GLN LYS GLY TYR GLN SEQRES 24 A 311 SER ILE ALA ASP PHE HIS GLY LYS LEU LYS SER LEU SEQRES 1 B 311 MET LEU ASN THR THR PHE ALA ASN ALA LYS PHE ALA ASN SEQRES 2 B 311 PRO PHE MET ASN ALA SER GLY VAL HIS CYS MET THR ILE SEQRES 3 B 311 GLU ASP LEU GLU GLU LEU LYS ALA SER GLN ALA GLY ALA SEQRES 4 B 311 TYR ILE THR LYS SER SER THR LEU GLU LYS ARG GLU GLY SEQRES 5 B 311 ASN PRO LEU ALA ARG TYR VAL ASP LEU GLU LEU GLY SER SEQRES 6 B 311 ILE ASN SER MET GLY LEU PRO ASN LEU GLY PHE ASP TYR SEQRES 7 B 311 TYR LEU ASP TYR VAL LEU LYS ASN GLN LYS GLU ASN ALA SEQRES 8 B 311 GLN GLU GLY PRO ILE PHE PHE SER ILE ALA GLY MET SER SEQRES 9 B 311 ALA ALA GLU ASN ILE ALA MET LEU LYS LYS ILE GLN GLU SEQRES 10 B 311 SER ASP PHE SER GLY ILE THR GLU LEU ASN LEU SER CYS SEQRES 11 B 311 PRO ASN VAL PRO GLY LYS PRO GLN LEU ALA TYR ASP PHE SEQRES 12 B 311 GLU ALA THR GLU LYS LEU LEU LYS GLU VAL PHE THR PHE SEQRES 13 B 311 PHE THR LYS PRO LEU GLY VAL LYS LEU PRO PRO TYR PHE SEQRES 14 B 311 ASP LEU VAL HIS PHE ASP ILE MET ALA GLU ILE LEU ASN SEQRES 15 B 311 GLN PHE PRO LEU THR TYR VAL ASN SER VAL ASN SER ILE SEQRES 16 B 311 GLY ASN GLY LEU PHE ILE ASP PRO GLU ALA GLU SER VAL SEQRES 17 B 311 VAL ILE LYS PRO LYS ASP GLY PHE GLY GLY ILE GLY GLY SEQRES 18 B 311 ALA TYR ILE LYS PRO THR ALA LEU ALA ASN VAL ARG ALA SEQRES 19 B 311 PHE TYR THR ARG LEU LYS PRO GLU ILE GLN ILE ILE GLY SEQRES 20 B 311 THR GLY GLY ILE GLU THR GLY GLN ASP ALA PHE GLU HIS SEQRES 21 B 311 LEU LEU CYS GLY ALA THR MET LEU GLN ILE GLY THR ALA SEQRES 22 B 311 LEU HIS LYS GLU GLY PRO ALA ILE PHE ASP ARG ILE ILE SEQRES 23 B 311 LYS GLU LEU GLU GLU ILE MET ASN GLN LYS GLY TYR GLN SEQRES 24 B 311 SER ILE ALA ASP PHE HIS GLY LYS LEU LYS SER LEU HET FMN A1312 31 HET ORO A1313 11 HET FMN B2312 31 HET ORO B2313 11 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM ORO OROTIC ACID HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 4 ORO 2(C5 H4 N2 O4) FORMUL 7 HOH *358(H2 O) HELIX 1 1 THR A 25 SER A 35 1 11 HELIX 2 2 GLY A 75 GLU A 89 1 15 HELIX 3 3 SER A 104 SER A 118 1 15 HELIX 4 4 GLN A 138 TYR A 141 5 4 HELIX 5 5 ASP A 142 PHE A 154 1 13 HELIX 6 6 ASP A 170 GLN A 183 1 14 HELIX 7 7 LYS A 211 ASP A 214 5 4 HELIX 8 8 GLY A 221 TYR A 223 5 3 HELIX 9 9 ILE A 224 THR A 237 1 14 HELIX 10 10 THR A 253 GLY A 264 1 12 HELIX 11 11 GLY A 271 GLY A 278 1 8 HELIX 12 12 ALA A 280 LYS A 296 1 17 HELIX 13 13 SER A 300 PHE A 304 5 5 HELIX 14 14 THR B 25 SER B 35 1 11 HELIX 15 15 GLY B 75 GLU B 89 1 15 HELIX 16 16 SER B 104 SER B 118 1 15 HELIX 17 17 GLN B 138 TYR B 141 5 4 HELIX 18 18 ASP B 142 PHE B 154 1 13 HELIX 19 19 ASP B 170 GLN B 183 1 14 HELIX 20 20 LYS B 211 ASP B 214 5 4 HELIX 21 21 GLY B 221 TYR B 223 5 3 HELIX 22 22 ILE B 224 THR B 237 1 14 HELIX 23 23 THR B 253 GLY B 264 1 12 HELIX 24 24 GLY B 271 GLY B 278 1 8 HELIX 25 25 ALA B 280 LYS B 296 1 17 HELIX 26 26 SER B 300 PHE B 304 5 5 SHEET 1 A 2 THR A 4 PHE A 6 0 SHEET 2 A 2 ALA A 9 PHE A 11 -1 O PHE A 11 N THR A 4 SHEET 1 B 7 PHE A 15 ASN A 17 0 SHEET 2 B 7 MET A 267 ILE A 270 1 O LEU A 268 N MET A 16 SHEET 3 B 7 GLN A 244 THR A 248 1 N GLY A 247 O MET A 267 SHEET 4 B 7 TYR A 188 SER A 191 1 N VAL A 189 O ILE A 246 SHEET 5 B 7 LEU A 161 LEU A 165 1 N VAL A 163 O ASN A 190 SHEET 6 B 7 ILE A 123 ASN A 127 1 N THR A 124 O GLY A 162 SHEET 7 B 7 PHE A 97 ILE A 100 1 N ILE A 100 O ASN A 127 SHEET 1 C 4 TYR A 58 LEU A 61 0 SHEET 2 C 4 GLY A 64 ASN A 67 -1 O GLY A 64 N LEU A 61 SHEET 3 C 4 PHE A 216 GLY A 220 -1 O GLY A 218 N ASN A 67 SHEET 4 C 4 ILE A 195 LEU A 199 -1 N ILE A 195 O ILE A 219 SHEET 1 D 2 ILE A 201 ASP A 202 0 SHEET 2 D 2 SER A 207 VAL A 208 -1 O SER A 207 N ASP A 202 SHEET 1 E 2 THR B 4 PHE B 6 0 SHEET 2 E 2 ALA B 9 PHE B 11 -1 O PHE B 11 N THR B 4 SHEET 1 F 7 PHE B 15 ASN B 17 0 SHEET 2 F 7 MET B 267 ILE B 270 1 O LEU B 268 N MET B 16 SHEET 3 F 7 GLN B 244 THR B 248 1 N GLY B 247 O GLN B 269 SHEET 4 F 7 TYR B 188 SER B 191 1 N VAL B 189 O ILE B 246 SHEET 5 F 7 LEU B 161 LEU B 165 1 N LEU B 165 O ASN B 190 SHEET 6 F 7 ILE B 123 ASN B 127 1 N LEU B 126 O GLY B 162 SHEET 7 F 7 PHE B 97 ILE B 100 1 N ILE B 100 O ASN B 127 SHEET 1 G 4 TYR B 58 LEU B 61 0 SHEET 2 G 4 GLY B 64 ASN B 67 -1 O GLY B 64 N LEU B 61 SHEET 3 G 4 PHE B 216 GLY B 220 -1 O GLY B 218 N ASN B 67 SHEET 4 G 4 ILE B 195 LEU B 199 -1 N ILE B 195 O ILE B 219 SHEET 1 H 2 ILE B 201 ASP B 202 0 SHEET 2 H 2 SER B 207 VAL B 208 -1 O SER B 207 N ASP B 202 SITE 1 AC1 20 ALA A 18 SER A 19 GLY A 20 LYS A 43 SITE 2 AC1 20 SER A 44 ASN A 67 ASN A 127 LYS A 164 SITE 3 AC1 20 VAL A 192 ASN A 193 GLY A 221 THR A 248 SITE 4 AC1 20 GLY A 249 GLY A 250 GLY A 271 THR A 272 SITE 5 AC1 20 ORO A1313 HOH A1315 HOH A1323 HOH A1335 SITE 1 AC2 11 LYS A 43 ASN A 67 MET A 69 GLY A 70 SITE 2 AC2 11 LEU A 71 ASN A 127 CYS A 130 PRO A 131 SITE 3 AC2 11 ASN A 193 SER A 194 FMN A1312 SITE 1 AC3 20 ALA B 18 SER B 19 GLY B 20 LYS B 43 SITE 2 AC3 20 SER B 44 ASN B 127 LYS B 164 VAL B 192 SITE 3 AC3 20 ASN B 193 GLY B 221 THR B 248 GLY B 249 SITE 4 AC3 20 GLY B 250 GLY B 271 THR B 272 ORO B2313 SITE 5 AC3 20 HOH B2317 HOH B2326 HOH B2332 HOH B2485 SITE 1 AC4 11 LYS B 43 ASN B 67 MET B 69 GLY B 70 SITE 2 AC4 11 LEU B 71 ASN B 127 CYS B 130 ASN B 193 SITE 3 AC4 11 SER B 194 FMN B2312 HOH B2484 CRYST1 53.074 108.822 66.453 90.00 103.92 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 0.018842 0.000000 0.004670 0.00000 SCALE2 0.000000 0.009189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015504 0.00000