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- PDB-6ebs: Crystal structure of Leishmania major dihydroorotate dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 6ebs
TitleCrystal structure of Leishmania major dihydroorotate dehydrogenase mutant H174A in complex with orotate
ComponentsDihydroorotate dehydrogenase (fumarate)Dihydroorotate dehydrogenase (fumarate)
KeywordsOXIDOREDUCTASE / dihydroorotate dehydrogenase / Leishmania major / mutant H174A
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleotide binding / nucleoplasm / cytoplasm
Similarity search - Function
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 domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / Roll / TIM Barrel ...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 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 / NICKEL (II) ION / OROTIC ACID / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsReis, R.A.G. / Pinheiro, M.P. / de Souza, A.L. / Hunter, W.N. / Nonato, M.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)11/23504-9 Brazil
Sao Paulo Research Foundation (FAPESP)07/08703-0 Brazil
CitationJournal: To Be Published
Title: Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant H174A in complex with orotate
Authors: Reis, R.A.G. / Pinheiro, M.P. / de Souza, A.L. / Hunter, W.N. / Nonato, M.C.
History
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (fumarate)
B: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,41317
Polymers76,1852
Non-polymers2,22815
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-112 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.279, 144.279, 69.913
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydroorotate dehydrogenase (fumarate) / Dihydroorotate dehydrogenase (fumarate) / Dihydroorotate oxidase


Mass: 38092.461 Da / Num. of mol.: 2 / Mutation: H174A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: DHODH, LMJF_16_0530 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q4QEW7, dihydroorotate dehydrogenase (fumarate)

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Non-polymers , 6 types, 511 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.1M sodium citrate tribasic dihydrate pH 5.9, 1.1M lithium sulfate, 0.3M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→46.58 Å / Num. obs: 52098 / % possible obs: 99.8 % / Redundancy: 7.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.136 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.05-2.113.30.4339350.805197.6
8.94-46.5880.0486690.999199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.505
Highest resolutionLowest resolution
Rotation41.65 Å2.14 Å

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
MOLREP11.5.05phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GYE

3gye


Resolution: 2.05→46.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.55 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.142 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 2480 4.8 %RANDOM
Rwork0.1658 ---
obs0.1677 49591 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.9 Å2 / Biso mean: 20.993 Å2 / Biso min: 2.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.05→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4689 0 146 525 5360
Biso mean--34.94 32.12 -
Num. residues----626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195050
X-RAY DIFFRACTIONr_angle_refined_deg1.05126870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4345654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7423.97199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97215800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9951528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213838
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 144 -
Rwork0.238 3585 -
all-3729 -
obs--97.49 %

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