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- PDB-1dor: DIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS -

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Basic information

Entry
Database: PDB / ID: 1dor
TitleDIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS
ComponentsDIHYDROOROTATE DEHYDROGENASE A
KeywordsOXIDOREDUCTASE / PYRIMIDINE NUCLEOTIDE BIOSYNTHESIS
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1 / Dihydroorotate Dehydrogenase A; chain A, domain 2 / Dihydroorotate Dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : ...Dihydroorotate dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1 / Dihydroorotate Dehydrogenase A; chain A, domain 2 / Dihydroorotate Dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase A (fumarate) / Dihydroorotate dehydrogenase A (fumarate)
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsRowland, P. / Larsen, S.
Citation
Journal: Structure / Year: 1997
Title: The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis.
Authors: Rowland, P. / Nielsen, F.S. / Jensen, K.F. / Larsen, S.
#1: Journal: Protein Sci. / Year: 1996
Title: Purification and Characterization of Dihydroorotate Dehydrogenase a from Lactococcus Lactis, Crystallization and Preliminary X-Ray Diffraction Studies of the Enzyme
Authors: Nielsen, F.S. / Rowland, P. / Larsen, S. / Jensen, K.F.
History
DepositionJan 14, 1997Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROOROTATE DEHYDROGENASE A
B: DIHYDROOROTATE DEHYDROGENASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3974
Polymers68,4842
Non-polymers9132
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-43 kcal/mol
Surface area22570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.190, 109.230, 67.170
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8728, 0.0049, 0.4881), (0.0052, -1, 0.0008), (0.4881, 0.0019, -0.8728)
Vector: -8.65, 64.2123, 32.4427)

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Components

#1: Protein DIHYDROOROTATE DEHYDROGENASE A


Mass: 34242.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lactococcus lactis (lactic acid bacteria)
References: UniProt: P54321, UniProt: A2RJT9*PLUS, EC: 1.3.3.1
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYSTEINE RESIDUES A 130 AND B 130 ARE PROBABLY OXIDIZED IN THIS CRYSTAL STRUCTURE. BOTH HAVE EXTRA ...CYSTEINE RESIDUES A 130 AND B 130 ARE PROBABLY OXIDIZED IN THIS CRYSTAL STRUCTURE. BOTH HAVE EXTRA SIDE CHAIN DENSITY BEYOND THEIR SG ATOMS, AND IN AN FO-FC DIFFERENCE MAP CALCULATED USING THE REFINED PROTEIN PHASES THE TWO LARGEST POSITIVE PEAKS CORRESPOND TO THESE POSITIONS. THESE TWO PEAKS ARE PROBABLY DUE TO A SINGLE OXYGEN ATOM COVALENTLY BONDED TO THE CYSTEINE SG ATOMS. THE COORDINATES OF THE TWO FO-FC PEAKS ARE AS FOLLOWS. A 130 PEAK (7.387,47.288,16.024) 2.4 ANGSTROMS FROM A 130 S B 130 PEAK (5.540,17.078,22.161) 2.1 ANGSTROMS FROM B 130 S ATOMS HAVE NOT BEEN INCLUDED IN THESE POSITIONS AND WERE NOT INCLUDED DURING ANY OF THE REFINEMENT STEPS. SEE MAIN JOURNAL REFERENCE FOR FURTHER DETAILS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLISED FROM A SOLUTION CONTAINING 30% PEG 6000, 0.2M SODIUM ACETATE AND 0.1M TRIS-HCL, PH 8.5.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %PEG60001reservoir
20.2 Msodium acetate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 50757 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 22.9 Å2 / Rsym value: 0.052 / Net I/σ(I): 22.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.234 / % possible all: 90.8
Reflection
*PLUS
Num. measured all: 179624 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 90.8 % / Rmerge(I) obs: 0.234

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2→25 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: R-FREE
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2060 4 %THIN SHELLS
Rwork0.168 ---
obs0.168 50732 99.3 %-
Displacement parametersBiso mean: 26.7 Å2
Refine analyzeLuzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 62 353 5233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.591
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.44
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.685
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it2.6
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2→2.03 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 103 4 %
Rwork0.253 2234 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM11.DNATOPH11.DNA
X-RAY DIFFRACTION4PARAM.FMNTOPOLOGY.FMN
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Num. reflection all: 50732 / Num. reflection obs: 48672
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.44
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.685

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