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- PDB-2b4g: dihydroorotate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2b4g
Titledihydroorotate dehydrogenase
Componentsdihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / glycosome / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / 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
BROMIDE ION / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsArakaki, T.L. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Mol.Microbiol. / Year: 2008
Title: Characterization of Trypanosoma brucei dihydroorotate dehydrogenase as a possible drug target; structural, kinetic and RNAi studies
Authors: Arakaki, T.L. / Buckner, F.S. / Gillespie, J.R. / Malmquist, N.A. / Phillips, M.A. / Kalyuzhniy, O. / Luft, J.R. / Detitta, G.T. / Verlinde, C.L. / Van Voorhis, W.C. / Hol, W.G. / Merritt, E.A.
History
DepositionSep 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Author states that electron density shows that residue 115 is definitely not an ALA. This ...SEQUENCE Author states that electron density shows that residue 115 is definitely not an ALA. This residue was modeled as a Val and it fits well with the electron density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dihydroorotate dehydrogenase
B: dihydroorotate dehydrogenase
C: dihydroorotate dehydrogenase
D: dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,59227
Polymers137,8954
Non-polymers3,69723
Water11,494638
1
A: dihydroorotate dehydrogenase
B: dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,83614
Polymers68,9472
Non-polymers1,88812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-37 kcal/mol
Surface area20770 Å2
MethodPISA
2
C: dihydroorotate dehydrogenase
D: dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,75613
Polymers68,9472
Non-polymers1,80911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-37 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.605, 162.630, 163.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
dihydroorotate dehydrogenase /


Mass: 34473.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb927.5.3830 / Plasmid: PET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q57U83, EC: 1.3.99.11

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Non-polymers , 5 types, 661 molecules

#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N2O4
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 638 / 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 Å3/Da / Density % sol: 36.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.4 ul protein 14.1 mg/ml 0.4 ul crystallization buffer, 40% PEG 1000, 0.1M Na Citrate, 0.1M KBr, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9201 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 5, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.95→163 Å / Num. obs: 76097 / % possible obs: 96.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID
1.95-2.060.4281.80.4281
2.06-2.180.2962.60.2961
2.18-2.330.2453.10.2451
2.33-2.520.2023.70.2021
2.52-2.760.154.90.151
2.76-3.080.1126.30.1121
3.08-3.560.0827.90.0821
3.56-4.360.0669.10.0661
4.36-6.170.06490.0641
6.17-20.880.0598.30.0591

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PDB_EXTRACT1.6data extraction
REFMACrefmac_5.2.0005 24/04/2001refinement
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB accession code 1JUE

1jue


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.562 / SU ML: 0.13 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24243 3814 5 %RANDOM
Rwork0.18894 ---
obs0.1916 72158 96 %-
all-75972 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--1.08 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9572 0 203 638 10413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210068
X-RAY DIFFRACTIONr_bond_other_d0.0010.029160
X-RAY DIFFRACTIONr_angle_refined_deg1.3262.00613669
X-RAY DIFFRACTIONr_angle_other_deg0.837321409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25551272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52124.36406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.928151679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8861546
X-RAY DIFFRACTIONr_chiral_restr0.0760.21510
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021953
X-RAY DIFFRACTIONr_nbd_refined0.1960.22055
X-RAY DIFFRACTIONr_nbd_other0.1780.29286
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24908
X-RAY DIFFRACTIONr_nbtor_other0.0830.25186
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.249
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7141.58063
X-RAY DIFFRACTIONr_mcbond_other0.1271.52565
X-RAY DIFFRACTIONr_mcangle_it0.821210093
X-RAY DIFFRACTIONr_scbond_it1.49534574
X-RAY DIFFRACTIONr_scangle_it2.2564.53563
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 192 -
Rwork0.265 4224 -
obs--76.52 %

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