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- PDB-3g2e: Structure of putative OORC subunit of 2-oxoglutarate:acceptor oxi... -

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Basic information

Entry
Database: PDB / ID: 3g2e
TitleStructure of putative OORC subunit of 2-oxoglutarate:acceptor oxidoreductase from Campylobacter jejuni
ComponentsOORC subunit of 2-oxoglutarate:acceptor oxidoreductase
KeywordsOXIDOREDUCTASE / structural genomics / OORC subunit of 2-oxoglutarate:acceptor oxidoreductase / oorC / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyPyruvate-ferredoxin Oxidoreductase; domain 3 / Pyruvate-ferredoxin oxidoreductase, PFOR, domain III / oxidoreductase activity, acting on the aldehyde or oxo group of donors / Pyruvate-flavodoxin oxidoreductase, central domain / Pyruvate/ketoisovalerate oxidoreductase, catalytic domain / Pyruvate ferredoxin/flavodoxin oxidoreductase / 3-Layer(aba) Sandwich / Alpha Beta / OORC subunit of 2-oxoglutarate:acceptor oxidoreductase
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsRamagopal, U.A. / Toro, R. / Miller, S. / Gilmore, M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of putative OORC subunit of 2-oxoglutarate:acceptor oxidoreductase from Campylobacter jejuni
Authors: Ramagopal, U.A. / Toro, R. / Miller, S. / Gilmore, M. / Burley, S.K. / Almo, S.C.
History
DepositionJan 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OORC subunit of 2-oxoglutarate:acceptor oxidoreductase
B: OORC subunit of 2-oxoglutarate:acceptor oxidoreductase
C: OORC subunit of 2-oxoglutarate:acceptor oxidoreductase
D: OORC subunit of 2-oxoglutarate:acceptor oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0935
Polymers85,0014
Non-polymers921
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12030 Å2
ΔGint-50 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.933, 70.170, 97.051
Angle α, β, γ (deg.)90.000, 92.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
OORC subunit of 2-oxoglutarate:acceptor oxidoreductase


Mass: 21250.318 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: Cj0538, oorC / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0PAX8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-tris pH 6.5, 25% PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 53857 / Num. obs: 53857 / % possible obs: 98.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.106 / Rsym value: 0.092 / Χ2: 1.051 / Net I/σ(I): 15.09
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.60.41152080.489196.8
2.07-2.154.20.33653730.5198.1
2.15-2.254.50.26853660.545198.3
2.25-2.374.50.21853240.597198.4
2.37-2.524.50.17953680.709198.6
2.52-2.714.50.14753880.856198.8
2.71-2.994.50.12153941.12198.9
2.99-3.424.50.09954261.645199.2
3.42-4.314.40.07954471.777199.2
4.31-504.20.07355632.12199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.857 / SU B: 3.744 / SU ML: 0.106 / SU R Cruickshank DPI: 0.178 / SU Rfree: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2732 5.1 %RANDOM
Rwork0.183 ---
obs0.186 53840 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.32 Å2 / Biso mean: 27.191 Å2 / Biso min: 10.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å21.04 Å2
2--0.16 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5618 0 6 382 6006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225740
X-RAY DIFFRACTIONr_angle_refined_deg1.311.977752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1825.193233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.497151023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8631520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214236
X-RAY DIFFRACTIONr_mcbond_it0.8341.53638
X-RAY DIFFRACTIONr_mcangle_it1.54725845
X-RAY DIFFRACTIONr_scbond_it2.39932102
X-RAY DIFFRACTIONr_scangle_it3.954.51904
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 174 -
Rwork0.22 3194 -
all-3368 -
obs--83.59 %

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