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- PDB-9yd7: Complex of Dihydroorotase from M. jannaschii with Carbamoyl Aspartate -

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Basic information

Entry
Database: PDB / ID: 9yd7
TitleComplex of Dihydroorotase from M. jannaschii with Carbamoyl Aspartate
ComponentsDihydroorotase
KeywordsHYDROLASE / complex / Dihydroorotase / TIM BARREL
Function / homology
Function and homology information


allantoinase activity / dihydroorotase / purine nucleobase catabolic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / zinc ion binding / cytoplasm
Similarity search - Function
Dihydroorotase / : / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
N-CARBAMOYL-L-ASPARTATE / Dihydroorotase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsVitali, J. / Nix, J.C. / Newman, H.E. / Colaneri, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071512 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169-01 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2026
Title: Crystal structure of Methanococcus jannaschii dihydroorotase with substrate bound.
Authors: Vitali, J. / Nix, J.C. / Newman, H.E. / Colaneri, M.J.
History
DepositionSep 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,12213
Polymers48,2261
Non-polymers89612
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.380, 111.380, 101.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Dihydroorotase / DHOase


Mass: 48226.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: PET-21A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami2 (DE3) / References: UniProt: Q58885, dihydroorotase
#2: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


Mass: 176.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N2O5
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.81 Å3/Da / Density % sol: 67.7 % / Description: hexagonal plate
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Reservoirs: 35% PEG400, 0.1 M Zn acetate and 0.1 M Na Mes pH 6.5. Drops: 2 ul protein 6.7 mg/ml, 1 ul reservoir, 0.5 ul dihydroorotate stock of 65 mM

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 11, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→48.23 Å / Num. obs: 59804 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.048 / Rrim(I) all: 0.129 / Net I/σ(I): 12.1
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.635 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3635 / CC1/2: 0.371 / Rpim(I) all: 0.764 / Rrim(I) all: 1.812 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→48.23 Å / SU ML: 0.179 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1826
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1863 2964 4.97 %
Rwork0.1685 56716 -
obs0.1694 59680 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.85 Å2
Refinement stepCycle: LAST / Resolution: 1.87→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 23 186 3598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753539
X-RAY DIFFRACTIONf_angle_d0.95554765
X-RAY DIFFRACTIONf_chiral_restr0.0607541
X-RAY DIFFRACTIONf_plane_restr0.0067607
X-RAY DIFFRACTIONf_dihedral_angle_d7.3022462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90.30671320.30492466X-RAY DIFFRACTION91.06
1.9-1.930.31021520.27262553X-RAY DIFFRACTION94.68
1.93-1.970.27371130.25552647X-RAY DIFFRACTION97.98
1.97-2.010.26651490.24192695X-RAY DIFFRACTION99.68
2.01-2.050.23541250.23482653X-RAY DIFFRACTION99.14
2.05-2.090.25761110.22132744X-RAY DIFFRACTION99.03
2.09-2.140.20461140.20052689X-RAY DIFFRACTION99.29
2.14-2.190.21581520.19062693X-RAY DIFFRACTION99.86
2.19-2.250.2111540.1832677X-RAY DIFFRACTION99.89
2.25-2.320.20511550.17532713X-RAY DIFFRACTION99.97
2.32-2.390.18671190.16242722X-RAY DIFFRACTION100
2.39-2.480.18381220.16772730X-RAY DIFFRACTION100
2.48-2.580.2071670.16742678X-RAY DIFFRACTION99.96
2.58-2.70.1931210.16972743X-RAY DIFFRACTION99.97
2.7-2.840.21591590.17232721X-RAY DIFFRACTION100
2.84-3.020.21871240.16792739X-RAY DIFFRACTION99.93
3.02-3.250.16451420.1592747X-RAY DIFFRACTION100
3.25-3.580.15251470.15122744X-RAY DIFFRACTION100
3.58-4.090.1571630.13332737X-RAY DIFFRACTION100
4.1-5.160.13752010.12662723X-RAY DIFFRACTION99.93
5.16-48.230.19521420.16842902X-RAY DIFFRACTION99.74

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