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- PDB-6dgs: Crystal Structure of Leishmania major dihydroorotate dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 6dgs
TitleCrystal Structure of Leishmania major dihydroorotate dehydrogenase mutant Y142A
ComponentsDihydroorotate dehydrogenase (fumarate)Dihydroorotate dehydrogenase (fumarate)
KeywordsOXIDOREDUCTASE / dihydroorotate dehydrogenase Leishmania major mutant Y142A
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 / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsReis, R.A.G. / Pinheiro, M.P. / 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 Y142A
Authors: Reis, R.A.G. / Pinheiro, M.P. / Nonato, M.C.
History
DepositionMay 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 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)77,4568
Polymers76,1672
Non-polymers1,2896
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-75 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.651, 140.651, 68.001
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 38083.434 Da / Num. of mol.: 2 / Mutation: Y142A
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)
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M sodium citrate tribasic dihydrate pH 5.6, 1.1M lithium sulfate, 0.45M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45868 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2016
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45868 Å / Relative weight: 1
ReflectionResolution: 1.75→121.807 Å / Num. obs: 77370 / % possible obs: 100 % / Redundancy: 7.8 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.116 / Rsym value: 0.109 / Net I/av σ(I): 4.9 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.75-1.844.80.6571.1112600.3390.7420.657100
1.84-1.965.80.4391.6106180.2010.4840.439100
1.96-2.096.50.2812.5100130.120.3060.281100
2.09-2.2680.1923.893190.0730.2060.192100
2.26-2.479.60.1644.385930.0560.1730.164100
2.47-2.779.30.1324.977610.0460.140.132100
2.77-3.29.60.1035.768940.0350.1080.103100
3.2-3.91100.0757.558340.0250.0790.075100
3.91-5.539.80.0658.445130.0220.0690.065100
5.53-48.8859.80.0648.525650.0210.0670.06499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.548
Highest resolutionLowest resolution
Rotation48.89 Å1.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALA3.3.22data scaling
MOLREP11.5.05phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GYE

3gye


Resolution: 1.75→121.807 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.172 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0932 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.09
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 3856 5 %RANDOM
Rwork0.1641 ---
obs0.1653 73474 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.92 Å2 / Biso mean: 21.106 Å2 / Biso min: 6.57 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.75→121.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 84 473 5161
Biso mean--20.94 30.37 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194945
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9916713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.82824.381210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59515822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3711527
X-RAY DIFFRACTIONr_chiral_restr0.0910.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213771
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 260 -
Rwork0.267 5440 -
all-5700 -
obs--100 %

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