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- PDB-3c61: Crystal structure of dihydroorotate dehydrogenase from Leishmania... -

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Basic information

Entry
Database: PDB / ID: 3c61
TitleCrystal structure of dihydroorotate dehydrogenase from Leishmania donovani
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / dihydroorotate dehydrogenase / leishmaniasis / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
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, 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
AZIDE ION / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsArakaki, T.L. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Dihydroorotate dehydrogenase from Leishmania donovani.
Authors: Arakaki, T.L. / Merritt, E.A. / Ullman, B. / Yates, P.A.
History
DepositionFeb 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)139,48130
Polymers136,0364
Non-polymers3,44526
Water13,547752
1
A: Dihydroorotate dehydrogenase
B: Dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,77916
Polymers68,0182
Non-polymers1,76114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
MethodPISA
2
C: Dihydroorotate dehydrogenase
D: Dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,70214
Polymers68,0182
Non-polymers1,68412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.869, 83.869, 188.725
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydroorotate dehydrogenase


Mass: 34008.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Plasmid: pET200 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0VWT2*PLUS, EC: 1.3.99.11

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Non-polymers , 7 types, 778 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#4: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 156.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N2O4
#6: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 2.545M Sodium chloride, 0.1M Citric acid, 5mM Orotic acid pH 5.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 5.2 % / Av σ(I) over netI: 9.1 / Number: 713271 / Rmerge(I) obs: 0.098 / Χ2: 0.91 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 137519 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.885099.910.0711.0435.9
3.083.8810010.0861.1085.7
2.693.0810010.0981.0435.3
2.442.6910010.1121.0855.2
2.272.4410010.1351.1035.1
2.132.2710010.161.0165
2.032.1310010.20.8125
1.942.0310010.2740.6825
1.861.9410010.3780.5985
1.81.8699.910.5150.5194.6
ReflectionResolution: 1.8→50 Å / Num. obs: 137519 / % possible obs: 100 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.098 / Χ2: 0.914 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.864.60.515137960.519199.9
1.86-1.9450.378137080.5981100
1.94-2.0350.274137350.6821100
2.03-2.1350.2137730.8121100
2.13-2.2750.16137741.0161100
2.27-2.445.10.135136901.1031100
2.44-2.695.20.112137821.0851100
2.69-3.085.30.098137401.0431100
3.08-3.885.70.086137471.1081100
3.88-505.90.071137741.043199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.01 Å37.75 Å
Translation2.01 Å37.75 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B4G

2b4g


Resolution: 1.8→33.88 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.096 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 6902 5 %RANDOM
Rwork0.166 ---
obs0.168 137496 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.249 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å20 Å2
2--0.27 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9532 0 212 752 10496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210279
X-RAY DIFFRACTIONr_bond_other_d0.0010.026884
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.99614029
X-RAY DIFFRACTIONr_angle_other_deg0.949316882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1651353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6624.388449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41151673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2461558
X-RAY DIFFRACTIONr_chiral_restr0.0810.21552
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022052
X-RAY DIFFRACTIONr_mcbond_it0.7511.56396
X-RAY DIFFRACTIONr_mcbond_other0.1921.52600
X-RAY DIFFRACTIONr_mcangle_it1.371210322
X-RAY DIFFRACTIONr_scbond_it2.25833883
X-RAY DIFFRACTIONr_scangle_it3.6524.53655
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 509 -
Rwork0.253 9631 -
all-10140 -
obs--99.86 %

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