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- PDB-6gdd: DIHYDROOROTASE FROM AQUIFEX AEOLICUS UNDER 1200 BAR OF HYDROSTATI... -

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Basic information

Entry
Database: PDB / ID: 6gdd
TitleDIHYDROOROTASE FROM AQUIFEX AEOLICUS UNDER 1200 BAR OF HYDROSTATIC PRESSURE
ComponentsDihydroorotase
KeywordsHYDROLASE / Dihydroorotase / Aquifex aeolicus / hydrostatic pressure / room temperature
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 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related ...Dihydroorotase / : / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsPrange, T. / Girard, E. / Herve, G. / Evans, D.R.
Citation
Journal: Febs J. / Year: 2019
Title: Pressure-induced activation of latent dihydroorotase from Aquifex aeolicus as revealed by high pressure protein crystallography.
Authors: Prange, T. / Girard, E. / Fourme, R. / Dhaussy, A.C. / Edwards, B. / Vaishnav, A. / Patel, C. / Guy-Evans, H. / Herve, G. / Evans, D.R.
#1: Journal: J. Biol. Chem. / Year: 2017
Title: Activation of latent dihydroorotase from aquifex aeolicus by pressure
Authors: Herve, G. / Guy-Evans, H. / Fernado, R. / Patel, C. / Hachem, F. / Evans, D.R.
History
DepositionApr 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6023
Polymers46,4411
Non-polymers1612
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.651, 176.148, 65.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Dihydroorotase / DHOase


Mass: 46440.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: pyrC, aq_806 / Production host: Escherichia coli (E. coli) / References: UniProt: O66990, dihydroorotase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.17 Å3/Da / Density % sol: 61.19 % / Description: prism
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ETHANOL (12%), PEG 400 (4%), ACETATE BUFFER (0.1M). PROTEIN 6 MG/ML

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID27 / Wavelength: 0.3738 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.3738 Å / Relative weight: 1
ReflectionResolution: 2.4→45.33 Å / Num. obs: 20901 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 49.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.062 / Net I/σ(I): 8.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3014 / Rpim(I) all: 0.46 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1XRF

1xrf


Resolution: 2.6→40.3 Å / Cor.coef. Fo:Fc: 0.965 / SU B: 6.238 / SU ML: 0.125 / Cross valid method: NONE / ESU R: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.15063 --
obs0.15063 16487 99.33 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.6→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 6 174 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0152950
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172830
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.7633982
X-RAY DIFFRACTIONr_angle_other_deg0.3961.7336637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3435373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94722.136103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.9915505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4821513
X-RAY DIFFRACTIONr_chiral_restr0.0610.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213205
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02479
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_it4.775.1421498
X-RAY DIFFRACTIONr_mcbond_other4.7385.1421497
X-RAY DIFFRACTIONr_mcangle_it6.6017.6931866
X-RAY DIFFRACTIONr_mcangle_other6.5997.6931867
X-RAY DIFFRACTIONr_scbond_it6.1345.8821452
X-RAY DIFFRACTIONr_scbond_other6.1315.8711446
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other98.4882108
X-RAY DIFFRACTIONr_long_range_B_refined10.97163.9513206
X-RAY DIFFRACTIONr_long_range_B_other10.96363.8033189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.27 1196 -
obs--99.75 %

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