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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 / homology
Function and homology information


dihydroorotate dehydrogenase (NAD+) / dihydroorotate dehydrogenase (NAD+) 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 / oxidoreductase activity / metal ion binding / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase B (pyrk subunit); domain 3 / Dihydroorotate dehydrogenase, electron transfer subunit / Dihydroorotate dehydrogenase electron transfer subunit / Dihydroorotate dehydrogenase, class 1B / : / Dihydroorotate dehydrogenase, electron transfer subunit, Fe-S binding domain superfamily / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / : / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B ...Dihydroorotate dehydrogenase B (pyrk subunit); domain 3 / Dihydroorotate dehydrogenase, electron transfer subunit / Dihydroorotate dehydrogenase electron transfer subunit / Dihydroorotate dehydrogenase, class 1B / : / Dihydroorotate dehydrogenase, electron transfer subunit, Fe-S binding domain superfamily / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / : / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Dihydroorotate dehydrogenase, class 1 / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Ribbon / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit / Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
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.
History
DepositionMar 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _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 B (PYRD SUBUNIT)
B: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1106
Polymers61,5362
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
Polymers123,0734
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 area14480 Å2
ΔGint-102 kcal/mol
Surface area41340 Å2
MethodPISA, PQS
Unit cell
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-MH32
Components on special symmetry positions
IDModelComponents
11A-1140-

HOH

21A-1141-

HOH

31A-1142-

HOH

41B-1143-

HOH

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 DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)


Mass: 32977.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P54322, EC: 1.3.3.1
#2: Protein DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)


Mass: 28559.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
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 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


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


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 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
IDConc.Common 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 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 31, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→38.5 Å / Num. all: 89776 / Num. obs: 21335 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4 % / Rmerge(I) obs: 0.497 / Num. unique all: 1107 / % possible all: 90.1
Reflection
*PLUS
Num. measured all: 89776

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.4→38.5 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1036 5 %Random
Rwork0.19 ---
all-21335 --
obs-21335 86 %-
Refinement stepCycle: LAST / Resolution: 2.4→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4255 0 99 144 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
Refinement
*PLUS
Lowest resolution: 38.5 Å / % reflection Rfree: 5 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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