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- PDB-6ed0: OhrA (Organic Hydroperoxide Resistance protein) mutant (C61S) in ... -

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Basic information

Entry
Database: PDB / ID: 6ed0
TitleOhrA (Organic Hydroperoxide Resistance protein) mutant (C61S) in the "open conformation" from chromobacterium violaceum
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / Ohr / thiol-proxidase
Function / homologyOrganic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology domain-like, alpha/beta / response to oxidative stress / Organic hydroperoxide resistance protein
Function and homology information
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2973
Polymers33,2012
Non-polymers961
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The protein was only found dimerized
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-71 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.963, 41.963, 123.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 141 / Label seq-ID: 21 - 161

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Organic hydroperoxide resistance protein


Mass: 16600.633 Da / Num. of mol.: 2 / Mutation: C61S
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 (bacteria) / References: UniProt: Q7P1K4
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: purified ohr protein at 10mg/ml in 5mM Tris-Hcl, pH 7.4 & 50mM NaCl) Crystallisation conditions: Ammonium sulfate 200mM, Sodium acetate 100mM pH 4, PEG 2,000 30%w/v

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.44→36.34 Å / Num. obs: 43151 / % possible obs: 97.9 % / Redundancy: 10.1 % / CC1/2: 1 / Rpim(I) all: 0.017 / Rrim(I) all: 0.038 / Net I/σ(I): 25.5
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 8.3 % / Num. unique obs: 1879 / CC1/2: 0.547 / Rpim(I) all: 1.261 / Rrim(I) all: 2.629 / % possible all: 84.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ECY

6ecy


Resolution: 1.44→35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.564 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21321 2048 4.8 %RANDOM
Rwork0.19135 ---
obs0.19239 41062 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.914 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.69 Å2-0 Å2
2--1.39 Å20 Å2
3----4.51 Å2
Refinement stepCycle: 1 / Resolution: 1.44→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 5 93 2181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132117
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172030
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.6382870
X-RAY DIFFRACTIONr_angle_other_deg1.4961.5714695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39121.53891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85715328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9141515
X-RAY DIFFRACTIONr_chiral_restr0.5410.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022431
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02414
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_it1.1581.951166
X-RAY DIFFRACTIONr_mcbond_other1.1531.951165
X-RAY DIFFRACTIONr_mcangle_it1.7092.9251454
X-RAY DIFFRACTIONr_mcangle_other1.712.9261455
X-RAY DIFFRACTIONr_scbond_it1.752.209951
X-RAY DIFFRACTIONr_scbond_other1.6692.199948
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5463.2071411
X-RAY DIFFRACTIONr_long_range_B_refined4.44523.8762156
X-RAY DIFFRACTIONr_long_range_B_other4.42223.7622150
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3682 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 143 -
Rwork0.352 2652 -
obs--86.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1137-0.22130.22121.0407-0.31023.66990.0659-0.2557-0.0094-0.0424-0.05040.04270.0315-0.1809-0.01550.00940.00010.00020.1116-0.01170.188672.8625.189824.7597
21.76370.16710.28321.1310.47794.26380.0863-0.17460.0673-0.186-0.10730.0565-0.0981-0.2990.0210.04870.0240.00190.0586-0.0020.180270.335627.936213.5501
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 142
2X-RAY DIFFRACTION2B1 - 142

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