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- PDB-6ecy: OhrA (Organic Hydroperoxide Resistance protein) wild type from ch... -

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Basic information

Entry
Database: PDB / ID: 6ecy
TitleOhrA (Organic Hydroperoxide Resistance protein) wild type from chromobacterium violaceum
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / Ohr / thiol-proxidase
Function / homology
Function and homology information


response to oxidative stress
Similarity search - Function
Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta ...Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Organic hydroperoxide resistance protein
Similarity search - Component
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDomingos, R.M. / Teixeira, R.D. / Alegria, T.G.P. / Netto, L.E.S.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)FAPESP: 2013/07937-8 Brazil
CitationJournal: Acs Catalysis / Year: 2020
Title: Substrate and product-assisted catalysis: molecular aspects behind structural switches along Organic Hydroperoxide Resistance Protein catalytic cycle
Authors: Domingos, R.M. / Teixeira, R.D. / Zeida, A. / Agudelo, W.A. / Alegria, T.G.P. / da Silva Neto, J.F. / Vieira, P.S. / Murakami, M.T. / Farah, C.S. / Estrin, D.A. / Netto, L.E.S.
History
DepositionAug 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Organic hydroperoxide resistance protein
B: Organic hydroperoxide resistance protein


Theoretical massNumber of molelcules
Total (without water)33,1692
Polymers33,1692
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The protein could only be found dimerized
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-48 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.094, 138.094, 45.116
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A0 - 141
2010B-1 - 141

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Components

#1: Protein Organic hydroperoxide resistance protein


Mass: 16584.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: ohr2, CV_0209 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7P1K4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
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: 3.74 Å3/Da / Density % sol: 67.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Purified OhrA protein 10mg/ml in 5mM Tris-Hcl pH 7.4 Crystallisation conditions: Potassium Sodium Tartrate 200mM, Tri-Sodium Citrate 100mM pH 5.5, Ammonium Sulfate 2M

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.4→36.01 Å / Num. obs: 94442 / % possible obs: 97.4 % / Redundancy: 19.7 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.017 / Rrim(I) all: 0.054 / Net I/σ(I): 26.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 19.3 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 92394 / CC1/2: 0.516 / Rpim(I) all: 1.241 / Rrim(I) all: 3.912 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N2F

1n2f


Resolution: 1.4→36 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.017 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.042 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17916 4705 5 %RANDOM
Rwork0.15132 ---
obs0.15272 89670 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.371 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å2-0 Å2
3----1.56 Å2
Refinement stepCycle: 1 / Resolution: 1.4→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 0 298 2429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132176
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172070
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.6342950
X-RAY DIFFRACTIONr_angle_other_deg1.5081.5714791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90421.56396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34315338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7361515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
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_it9.1262.9941194
X-RAY DIFFRACTIONr_mcbond_other9.0992.9931193
X-RAY DIFFRACTIONr_mcangle_it7.0514.4951489
X-RAY DIFFRACTIONr_mcangle_other7.064.4961490
X-RAY DIFFRACTIONr_scbond_it6.8293.71982
X-RAY DIFFRACTIONr_scbond_other6.8263.71983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3115.2771462
X-RAY DIFFRACTIONr_long_range_B_refined8.11738.8152308
X-RAY DIFFRACTIONr_long_range_B_other8.02338.1832262
X-RAY DIFFRACTIONr_rigid_bond_restr14.25134244
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3528 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 333 -
Rwork0.342 6757 -
obs--99.8 %

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