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

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Basic information

Entry
Database: PDB / ID: 6dwg
TitleCrystal structure of Leishmania major dihydroorotate dehydrogenase mutant Q139A
ComponentsDihydroorotate dehydrogenase (fumarate)
KeywordsOXIDOREDUCTASE / dihydroorotate dehydrogenase / Leishmania major / mutant Q139A
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 ...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 / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 Q139A
Authors: Reis, R.A.G. / Pinheiro, M.P. / Nonato, M.C.
History
DepositionJun 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 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)77,83312
Polymers76,2052
Non-polymers1,62810
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-82 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.469, 143.469, 69.737
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 oxidase


Mass: 38102.477 Da / Num. of mol.: 2 / Mutation: Q139A
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 , 5 types, 392 molecules

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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
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: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2014
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.9→46.96 Å / Num. obs: 64497 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.025 / Rrim(I) all: 0.06 / Net I/σ(I): 18.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.3 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.940.3841400.90.180.42299.9
9.11-46.960.036240.9980.0140.03498.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.509
Highest resolutionLowest resolution
Rotation46.96 Å2.11 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.5.15data scaling
MOLREP11.5.05phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GYE

3gye


Resolution: 1.9→46.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.701 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.111 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.195 3207 5 %RANDOM
Rwork0.174 ---
obs0.175 61257 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4589 0 102 382 5073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195026
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9866847
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4785664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.25324.129201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60315797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0181525
X-RAY DIFFRACTIONr_chiral_restr0.0850.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213829
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 202 -
Rwork0.273 4522 -
obs--99.87 %

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