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- PDB-4wzh: Dihydroorotate dehydrogenase from Leishmania Viannia braziliensis -

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Basic information

Entry
Database: PDB / ID: 4wzh
TitleDihydroorotate dehydrogenase from Leishmania Viannia braziliensis
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE / Dihydroorotate dehydrogenase
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase A, chain A, domain 2 / 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 ...Dihydroorotate dehydrogenase A, chain A, domain 2 / 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 braziliensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsReis, R.A.G. / Lorenzato, E. / Silva, V.C. / Nonato, M.C.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/25075-0 Brazil
Sao Paulo Research Foundation (FAPESP)2014/01257-8 Brazil
Sao Paulo Research Foundation (FAPESP)2011/23504-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)159061/2012-1 Brazil
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Recombinant production, crystallization and crystal structure determination of dihydroorotate dehydrogenase from Leishmania (Viannia) braziliensis.
Authors: Reis, R.A. / Lorenzato, E. / Silva, V.C. / Nonato, M.C.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
B: Dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0476
Polymers74,8042
Non-polymers1,2434
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-41 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.160, 105.690, 106.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dihydroorotate dehydrogenase


Mass: 37401.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania braziliensis (eukaryote) / Gene: DHODH, LBRM_16_0550 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E9AI53, dihydroorotate dehydrogenase (fumarate)
#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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45866 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45866 Å / Relative weight: 1
ReflectionResolution: 2.12→40.1 Å / Num. all: 39526 / Num. obs: 39159 / % possible obs: 99.3 % / Redundancy: 11 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.231 / Net I/σ(I): 2
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.233 / Mean I/σ(I) obs: 2 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GYE

3gye


Resolution: 2.12→33.579 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 1975 5.04 %Random selection
Rwork0.1765 ---
obs0.1789 39159 98.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.12→33.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 83 267 4908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084759
X-RAY DIFFRACTIONf_angle_d1.1016451
X-RAY DIFFRACTIONf_dihedral_angle_d13.6711693
X-RAY DIFFRACTIONf_chiral_restr0.042700
X-RAY DIFFRACTIONf_plane_restr0.005828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.1730.32271420.28012530X-RAY DIFFRACTION95
2.173-2.23180.34671320.30422352X-RAY DIFFRACTION89
2.2318-2.29740.29991350.25672547X-RAY DIFFRACTION96
2.2974-2.37150.25711510.22412626X-RAY DIFFRACTION99
2.3715-2.45630.24241340.21022661X-RAY DIFFRACTION99
2.4563-2.55460.28831260.21142673X-RAY DIFFRACTION100
2.5546-2.67080.27411370.20772673X-RAY DIFFRACTION100
2.6708-2.81160.25731340.19452673X-RAY DIFFRACTION100
2.8116-2.98760.22181430.18472700X-RAY DIFFRACTION100
2.9876-3.21810.24021640.18292697X-RAY DIFFRACTION100
3.2181-3.54160.19081300.15892693X-RAY DIFFRACTION100
3.5416-4.05340.18241510.13872731X-RAY DIFFRACTION100
4.0534-5.10390.17421490.12332740X-RAY DIFFRACTION100
5.1039-33.58270.21041470.16632888X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 3.2198 Å / Origin y: 20.3973 Å / Origin z: 31.2305 Å
111213212223313233
T0.2056 Å2-0.0502 Å20.0102 Å2-0.2551 Å2-0.0118 Å2--0.2206 Å2
L0.4969 °2-0.3455 °20.1532 °2-1.5958 °20.5248 °2--0.7455 °2
S0.0461 Å °0.1188 Å °-0.0907 Å °-0.1511 Å °0.0995 Å °-0.1855 Å °-0.0086 Å °0.1334 Å °-0.1435 Å °
Refinement TLS groupSelection details: all

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