HEADER OXIDOREDUCTASE 23-MAY-05 2BSL TITLE CRYSTAL STRUCTURE OF L. LACTIS DIHYDROOROTATE DEHYDROGENSE A IN TITLE 2 COMPLEX WITH 3,4-DIHYDROXYBENZOATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DIHYDROOROTATE DEHYDROGENSE, DHOD A, DIHYDROOROTATE OXIDASE COMPND 5 A, DHODEHASE A, DHODASE A; COMPND 6 EC: 1.3.99.11; COMPND 7 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 KEYWDS NUCLEOTIDE METABOLISM, DIHYDROOROTATE DEHYDROGENASE, FMN, KEYWDS 2 FLAVOPROTEIN, OXIDOREDUCTASE, PYRIMIDINE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR A.E.WOLFE,M.HANSEN,S.G.GATTIS,Y.-C.HU,E.JOHANSSON,S.ARENT,S.LARSEN, AUTHOR 2 B.A.PALFEY REVDAT 6 13-DEC-23 2BSL 1 LINK REVDAT 5 08-MAY-19 2BSL 1 REMARK REVDAT 4 24-FEB-09 2BSL 1 VERSN REVDAT 3 22-MAY-07 2BSL 1 JRNL REVDAT 2 01-MAY-07 2BSL 1 AUTHOR JRNL REVDAT 1 29-AUG-06 2BSL 0 JRNL AUTH A.E.WOLFE,M.THYMARK,S.G.GATTIS,R.L.FAGAN,Y.-C.HU, JRNL AUTH 2 E.JOHANSSON,S.ARENT,S.LARSEN,B.A.PALFEY JRNL TITL INTERACTION OF BENZOATE PYRIMIDINE ANALOGUES WITH CLASS 1A JRNL TITL 2 DIHYDROOROTATE DEHYDROGENASE FROM LACTOCOCCUS LACTIS. JRNL REF BIOCHEMISTRY V. 46 5741 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17444658 JRNL DOI 10.1021/BI7001554 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 27913 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1526 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) : 1526 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4818 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.63000 REMARK 3 B22 (A**2) : -4.28000 REMARK 3 B33 (A**2) : -2.67000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.68000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.366 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.248 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.164 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.805 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 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): 5007 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4501 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6777 ; 1.687 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10557 ; 0.925 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 620 ; 7.047 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 744 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5523 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 937 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1045 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5108 ; 0.234 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2763 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 195 ; 0.170 ; 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): 1 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 18 ; 0.215 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.066 ; 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): 3093 ; 0.809 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4970 ; 1.505 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1914 ; 2.294 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1807 ; 3.778 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 128 2 REMARK 3 1 B 1 B 128 2 REMARK 3 2 A 140 A 312 2 REMARK 3 2 B 140 B 312 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1759 ; 0.04 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 2776 ; 0.26 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 1759 ; 0.17 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2776 ; 0.66 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2BSL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1290023991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32557 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.9000 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) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1OVD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17 MG/ML PROTEIN AND 2.6 MM 3, 4-DIOHB REMARK 280 HANGING DROPS 2 MICROLITERS OF PROTEIN AND 2 MICROLITERS REMARK 280 RESERVOIR: 30 % PEG 6000, 1 MM DTT, 0.2 M SODIUM ACETATE AND 0.1 REMARK 280 M TRIS-HCL PH 8.5, PH 8.50, VAPOR DIFFUSION, HANGING DROP 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 54.08000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 CATALYSIS: (S)-DIHYDROOROTATE + O2 => OROTATE + H2O2 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 O HOH A 2016 O HOH A 2040 2.12 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 ASP A 81 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 283 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP B 81 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 7 55.32 36.71 REMARK 500 CYS A 23 24.69 -150.29 REMARK 500 SER A 129 27.31 -153.14 REMARK 500 GLN A 138 114.60 -36.87 REMARK 500 PRO A 185 47.76 -80.59 REMARK 500 GLU A 252 -33.96 -138.82 REMARK 500 ASN B 8 15.03 58.17 REMARK 500 CYS B 23 25.88 -147.60 REMARK 500 SER B 129 14.03 -152.96 REMARK 500 PRO B 185 49.38 -79.42 REMARK 500 TYR B 223 -39.34 -37.92 REMARK 500 GLU B 252 -35.01 -136.17 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 MG A1314 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 33 O REMARK 620 2 SER A 35 O 90.6 REMARK 620 3 HOH A2013 O 149.5 85.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1314 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 33 O REMARK 620 2 SER B 35 O 86.3 REMARK 620 3 HOH B2013 O 161.6 88.0 REMARK 620 4 HOH B2014 O 82.7 75.4 78.9 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 ACT A1313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1314 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1314 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A1312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B1312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DHB B1313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1315 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DOR RELATED DB: PDB REMARK 900 DIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS REMARK 900 RELATED ID: 1JQV RELATED DB: PDB REMARK 900 THE K213E MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATEDEHYDROGENASE A REMARK 900 RELATED ID: 1JQX RELATED DB: PDB REMARK 900 THE R57A MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATEDEHYDROGENASE A REMARK 900 RELATED ID: 1JRB RELATED DB: PDB REMARK 900 THE P56A MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATEDEHYDROGENASE A REMARK 900 RELATED ID: 1JRC RELATED DB: PDB REMARK 900 THE N67A MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATEDEHYDROGENASE A REMARK 900 RELATED ID: 1JUB RELATED DB: PDB REMARK 900 THE K136E MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATEDEHYDROGENASE A REMARK 900 RELATED ID: 1JUE RELATED DB: PDB REMARK 900 1.8 A RESOLUTION STRUCTURE OF NATIVE LACTOCOCCUS REMARK 900 LACTISDIHYDROOROTATE DEHYDROGENASE A REMARK 900 RELATED ID: 1NFC RELATED DB: PDB REMARK 900 STRUCTURE OF DIHYDROOROTATE DEHYDROGENASE A OF LACTOCOCCUSLACTIS REMARK 900 RELATED ID: 1OVD RELATED DB: PDB REMARK 900 THE K136E MUTANT OF LACTOCOCCUS LACTIS DIHYDROOROTATEDEHYDROGENASE REMARK 900 A IN COMPLEX WITH OROTATE REMARK 900 RELATED ID: 2DOR RELATED DB: PDB REMARK 900 DIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS COMPLEXED REMARK 900 WITH OROTATE DBREF 2BSL A 1 311 UNP P54321 PYRDA_LACLC 1 311 DBREF 2BSL B 1 311 UNP P54321 PYRDA_LACLC 1 311 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 PRO 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 PRO 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 ACT A1313 4 HET MG A1314 1 HET GOL A1315 6 HET FMN B1312 31 HET DHB B1313 11 HET MG B1314 1 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM ACT ACETATE ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM DHB 3,4-DIHYDROXYBENZOIC ACID HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 MG 2(MG 2+) FORMUL 6 GOL C3 H8 O3 FORMUL 8 DHB C7 H6 O4 FORMUL 10 HOH *165(H2 O) HELIX 1 1 THR A 25 SER A 35 1 11 HELIX 2 2 GLY A 75 ASN A 90 1 16 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 ASN A 182 1 13 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 GLY A 297 1 18 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 ASN B 90 1 16 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 PHE B 216 5 6 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 AA 2 THR A 4 PHE A 6 0 SHEET 2 AA 2 ALA A 9 PHE A 11 -1 O ALA A 9 N PHE A 6 SHEET 1 AB 7 PHE A 15 ASN A 17 0 SHEET 2 AB 7 MET A 267 ILE A 270 1 O LEU A 268 N MET A 16 SHEET 3 AB 7 GLN A 244 THR A 248 1 O GLY A 247 N GLN A 269 SHEET 4 AB 7 TYR A 188 SER A 191 1 O VAL A 189 N ILE A 246 SHEET 5 AB 7 LEU A 161 LEU A 165 1 O VAL A 163 N ASN A 190 SHEET 6 AB 7 ILE A 123 ASN A 127 1 O THR A 124 N GLY A 162 SHEET 7 AB 7 PHE A 97 ILE A 100 1 O PHE A 98 N GLU A 125 SHEET 1 AC 4 TYR A 58 LEU A 61 0 SHEET 2 AC 4 GLY A 64 ASN A 67 -1 O GLY A 64 N LEU A 61 SHEET 3 AC 4 PHE A 216 GLY A 220 -1 O GLY A 218 N ASN A 67 SHEET 4 AC 4 ILE A 195 LEU A 199 -1 O ILE A 195 N ILE A 219 SHEET 1 AD 2 ILE A 201 ASP A 202 0 SHEET 2 AD 2 SER A 207 VAL A 208 -1 O SER A 207 N ASP A 202 SHEET 1 BA 2 THR B 4 PHE B 6 0 SHEET 2 BA 2 ALA B 9 PHE B 11 -1 O ALA B 9 N PHE B 6 SHEET 1 BB 7 PHE B 15 ASN B 17 0 SHEET 2 BB 7 MET B 267 ILE B 270 1 O LEU B 268 N MET B 16 SHEET 3 BB 7 GLN B 244 THR B 248 1 O GLY B 247 N GLN B 269 SHEET 4 BB 7 TYR B 188 SER B 191 1 O VAL B 189 N ILE B 246 SHEET 5 BB 7 LEU B 161 LEU B 165 1 O VAL B 163 N ASN B 190 SHEET 6 BB 7 ILE B 123 ASN B 127 1 O THR B 124 N GLY B 162 SHEET 7 BB 7 PHE B 97 ILE B 100 1 O PHE B 98 N GLU B 125 SHEET 1 BC 4 TYR B 58 LEU B 61 0 SHEET 2 BC 4 GLY B 64 ASN B 67 -1 O GLY B 64 N LEU B 61 SHEET 3 BC 4 GLY B 217 GLY B 220 -1 O GLY B 218 N ASN B 67 SHEET 4 BC 4 ILE B 195 GLY B 198 -1 O ILE B 195 N ILE B 219 SHEET 1 BD 2 ILE B 201 ASP B 202 0 SHEET 2 BD 2 SER B 207 VAL B 208 -1 O SER B 207 N ASP B 202 LINK O LYS A 33 MG MG A1314 1555 1555 2.33 LINK O SER A 35 MG MG A1314 1555 1555 2.39 LINK MG MG A1314 O HOH A2013 1555 1555 2.64 LINK O LYS B 33 MG MG B1314 1555 1555 2.27 LINK O SER B 35 MG MG B1314 1555 1555 2.43 LINK MG MG B1314 O HOH B2013 1555 1555 2.54 LINK MG MG B1314 O HOH B2014 1555 1555 2.57 CISPEP 1 LEU A 55 PRO A 56 0 -1.48 CISPEP 2 SER A 191 VAL A 192 0 5.12 CISPEP 3 LEU B 55 PRO B 56 0 -2.75 CISPEP 4 SER B 191 VAL B 192 0 4.99 SITE 1 AC1 8 ASN A 127 CYS A 130 PRO A 131 ASN A 193 SITE 2 AC1 8 FMN A1312 HOH A2016 HOH A2040 HOH A2048 SITE 1 AC2 3 LYS A 33 SER A 35 HOH A2013 SITE 1 AC3 4 LYS B 33 SER B 35 HOH B2013 HOH B2014 SITE 1 AC4 21 ALA A 18 SER A 19 GLY A 20 LYS A 43 SITE 2 AC4 21 SER A 44 ASN A 67 ASN A 127 LYS A 164 SITE 3 AC4 21 VAL A 192 ASN A 193 GLY A 221 THR A 248 SITE 4 AC4 21 GLY A 249 GLY A 250 GLY A 271 THR A 272 SITE 5 AC4 21 ACT A1313 HOH A2039 HOH A2047 HOH A2087 SITE 6 AC4 21 HOH A2088 SITE 1 AC5 21 ALA B 18 SER B 19 GLY B 20 LYS B 43 SITE 2 AC5 21 SER B 44 ASN B 67 ASN B 127 LYS B 164 SITE 3 AC5 21 VAL B 192 ASN B 193 SER B 194 GLY B 221 SITE 4 AC5 21 THR B 248 GLY B 249 GLY B 250 GLY B 271 SITE 5 AC5 21 THR B 272 DHB B1313 HOH B2033 HOH B2067 SITE 6 AC5 21 HOH B2077 SITE 1 AC6 12 LYS B 43 MET B 69 GLY B 70 LEU B 71 SITE 2 AC6 12 PRO B 72 ASN B 127 CYS B 130 PRO B 131 SITE 3 AC6 12 ASN B 132 ASN B 193 SER B 194 FMN B1312 SITE 1 AC7 5 TYR A 168 PHE A 169 HIS A 173 TYR B 141 SITE 2 AC7 5 HIS B 173 CRYST1 53.588 108.160 66.222 90.00 104.06 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 0.018661 0.000000 0.004672 0.00000 SCALE2 0.000000 0.009246 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015567 0.00000 MTRIX1 1 0.878740 0.009773 0.477190 -8.47970 1 MTRIX2 1 0.009773 -0.999950 0.002482 64.39900 1 MTRIX3 1 0.477190 0.002482 -0.878800 32.06600 1