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- PDB-1ep2: CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGEN... -

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Basic information

Entry
Database: PDB / ID: 1ep2
TitleCRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B COMPLEXED WITH OROTATE
Components(DIHYDROOROTATE DEHYDROGENASE B ...) x 2
KeywordsOXIDOREDUCTASE / Heterotetramer
Function / homologyAldolase-type TIM barrel / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Riboflavin synthase-like beta-barrel / FAD-binding domain, ferredoxin reductase-type / Dihydroorotate dehydrogenase, class 1B / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase domain / Oxidoreductase FAD/NAD(P)-binding ...Aldolase-type TIM barrel / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Riboflavin synthase-like beta-barrel / FAD-binding domain, ferredoxin reductase-type / Dihydroorotate dehydrogenase, class 1B / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase domain / Oxidoreductase FAD/NAD(P)-binding / Phthalate dioxygenase reductase / Dihydroorotate dehydrogenase, class 1 / Dihydroorotate dehydrogenase, electron transfer subunit, Fe-S binding domain superfamily / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Oxidoreductase NAD-binding domain / Dihydroorotate dehydrogenase / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Ferredoxin reductase-type FAD binding domain profile. / Dihydroorotate dehydrogenase electron transfer subunit / dihydroorotate dehydrogenase (NAD+) / orotate reductase (NADH) activity / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / electron transfer activity / metal ion binding / cytoplasm / Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit / Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
Function and homology information
Specimen sourceLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / 2.4 Å resolution
AuthorsRowland, P. / Norager, S. / Jensen, K.F. / Larsen, S.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster.
Authors: Rowland, P. / Norager, S. / Jensen, K.F. / Larsen, S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 27, 2000 / Release: Jan 17, 2001
RevisionDateData content typeGroupProviderType
1.0Jan 17, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
B: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1106
Polyers61,5362
Non-polymers1,5744
Water2,594144
1
A: DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
B: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
hetero molecules

A: DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
B: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,22012
Polyers123,0734
Non-polymers3,1488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area (Å2)14480
ΔGint (kcal/M)-102
Surface area (Å2)41340
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)202.420, 202.420, 80.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH 3 2
DetailsThe biological assembly is a heterotetramer. There is a crystallographic two-fold axis through the center of the heterotetramer, passing through a small hydrophobic cavity between the two chain A molecules of the heterotetramer at approximate coordinates (47.61, 34.32, 13.52). The heterotetramer is held together by the two chain A molecules, with the two chain B molecules making few close contacts with each other.

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Components

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DIHYDROOROTATE DEHYDROGENASE B ... , 2 types, 2 molecules AB

#1: Protein/peptide DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)


Mass: 32977.289 Da / Num. of mol.: 1
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Genus: Lactococcus / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P54322, EC: 1.3.3.1
#2: Protein/peptide DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)


Mass: 28559.100 Da / Num. of mol.: 1
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Genus: Lactococcus / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P56968, EC: 1.3.3.1

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Non-polymers , 5 types, 148 molecules

#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Formula: C17H21N4O9P / Flavin mononucleotide
#4: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / Formula: C5H4N2O4 / Orotic acid
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Formula: C27H33N9O15P2 / Flavin adenine dinucleotide / Comment: FAD *YM
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Formula: Fe2S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Formula: H2O / Water

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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: 2.59 / Density percent sol: 52.5 %
Crystal growTemp: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.4 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6
Details: Rowland, P., (1997) Acta Crystallogr., Sect.D, 53, 802.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
120 mg/mlprotein1drop
250 mMsodium phosphate1drop
310 %glycerol1drop
42.4 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 288 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Collection date: Jan 31, 1997
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 34 Å2 / D resolution high: 2.4 Å / D resolution low: 38.5 Å / Number all: 89776 / Number obs: 21335 / Observed criterion sigma I: -3 / Rmerge I obs: 0.099 / NetI over sigmaI: 12.4 / Redundancy: 4.2 % / Percent possible obs: 86
Reflection shellRmerge I obs: 0.497 / Highest resolution: 2.4 Å / Lowest resolution: 2.44 Å / Number unique all: 1107 / Redundancy: 4 % / Percent possible all: 90.1
Reflection
*PLUS
Number measured all: 89776

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefineR Free selection details: Random / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.241 / R factor R work: 0.19 / Highest resolution: 2.4 Å / Lowest resolution: 38.5 Å / Number reflection R free: 1036 / Number reflection all: 21335 / Number reflection obs: 21335 / Percent reflection R free: 5 / Percent reflection obs: 86
Refine hist #LASTHighest resolution: 2.4 Å / Lowest resolution: 38.5 Å
Number of atoms included #LASTProtein: 4255 / Nucleic acid: 0 / Ligand: 99 / Solvent: 144 / Total: 4498
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.639
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Least-squares process
*PLUS
R factor R work: 0.19 / R factor obs: 0.19 / Lowest resolution: 38.5 Å / Percent reflection R free: 5

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