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- PDB-6ebc: OhrB (Organic Hydroperoxide Resistance protein) wild type from Ch... -

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Basic information

Entry
Database: PDB / ID: 6ebc
TitleOhrB (Organic Hydroperoxide Resistance protein) wild type from Chromobacterium violaceum and reduced by DTT
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 / N-terminal domain of TfIIb - #10 / K homology (KH) domain / 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 / N-terminal domain of TfIIb - #10 / K homology (KH) domain / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Organic hydroperoxide resistance protein
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsDomingos, R.M. / Teixeira, R.D. / Alegria, T.G.P. / Vieira, P.S. / Murakami, M.T. / 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 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Organic hydroperoxide resistance protein
B: Organic hydroperoxide resistance protein
C: Organic hydroperoxide resistance protein
D: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,12314
Polymers67,4124
Non-polymers71110
Water4,342241
1
A: Organic hydroperoxide resistance protein
C: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0027
Polymers33,7062
Non-polymers2965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-41 kcal/mol
Surface area12380 Å2
MethodPISA
2
B: Organic hydroperoxide resistance protein
D: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1217
Polymers33,7062
Non-polymers4155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-52 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.160, 88.160, 169.916
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA2 - 14022 - 160
21SERSERLEULEUBB2 - 14022 - 160
12SERSERALAALAAA2 - 14122 - 161
22SERSERALAALACC2 - 14122 - 161
13SERSERLEULEUAA2 - 14022 - 160
23SERSERLEULEUDD2 - 14022 - 160
14SERSERLEULEUBB2 - 14022 - 160
24SERSERLEULEUCC2 - 14022 - 160
15HISHISLEULEUBB0 - 14020 - 160
25HISHISLEULEUDD0 - 14020 - 160
16SERSERLEULEUCC2 - 14022 - 160
26SERSERLEULEUDD2 - 14022 - 160

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Organic hydroperoxide resistance protein


Mass: 16852.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CBW21_15220 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A202B6V5
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Cl
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: Purified protein 10mg/ml in 5mM Tris-Hcl, pH 7.4 and DTT 10mM Crystallization solution: Magnesium Chloride 200mM, BIS-TRIS 100mM pH 5.5, PEG 3,350 25%w/v Then, Soaked with Cs + DTT 50mM

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Data collection

DiffractionMean temperature: 273.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.45866 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45866 Å / Relative weight: 1
ReflectionResolution: 1.87→45.49 Å / Num. obs: 61621 / % possible obs: 100 % / Redundancy: 17.2 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Rrim(I) all: 0.114 / Net I/σ(I): 19
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 9.3 % / Num. unique obs: 3977 / CC1/2: 0.356 / Rpim(I) all: 1.275 / Rrim(I) all: 2.798 / % 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: 6EB4

6eb4


Resolution: 1.87→35 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.02 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21446 3029 4.9 %RANDOM
Rwork0.19308 ---
obs0.19415 58510 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.783 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å2-0 Å2
3----1.94 Å2
Refinement stepCycle: 1 / Resolution: 1.87→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 31 241 4394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134197
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173975
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.6425670
X-RAY DIFFRACTIONr_angle_other_deg1.5111.5739207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.975561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1821.188202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94815685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3931536
X-RAY DIFFRACTIONr_chiral_restr0.080.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02857
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_it1.7052.5762256
X-RAY DIFFRACTIONr_mcbond_other1.7032.5762255
X-RAY DIFFRACTIONr_mcangle_it2.7393.8552813
X-RAY DIFFRACTIONr_mcangle_other2.7393.8562814
X-RAY DIFFRACTIONr_scbond_it2.1822.9591941
X-RAY DIFFRACTIONr_scbond_other2.1832.961942
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4254.2842858
X-RAY DIFFRACTIONr_long_range_B_refined6.48432.9864946
X-RAY DIFFRACTIONr_long_range_B_other6.4732.5444870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A38540.12
12B38540.12
21A38920.12
22C38920.12
31A38870.11
32D38870.11
41B39480.1
42C39480.1
51B39040.12
52D39040.12
61C38800.11
62D38800.11
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 236 -
Rwork0.328 4311 -
obs--99.93 %
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)
13.0347-1.61990.11283.34890.27083.1597-0.1591-0.3143-0.13410.35120.13750.190.1529-0.04210.02160.0460.01460.01070.03450.0070.0329-53.888912.9812-28.5443
24.34940.70040.6972.28110.42681.69460.09410.05340.08150.0937-0.02920.18790.1329-0.132-0.0650.0522-0.0362-0.02310.03980.01510.044-25.592630.0838-23.1462
32.5843-0.74720.65963.0024-0.14542.54440.07210.0649-0.243-0.0794-00.0740.27540.0927-0.07210.03140.0087-0.00770.0086-0.00760.0232-48.91496.1805-38.0076
44.26041.10621.20971.5501-0.11642.7473-0.06040.5014-0.0802-0.07910.13460.03120.0490.2294-0.07430.022-0.0325-0.0220.10990.00850.0578-17.311531.5817-32.0413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 141
2X-RAY DIFFRACTION2B-1 - 141
3X-RAY DIFFRACTION3C2 - 141
4X-RAY DIFFRACTION4D0 - 141

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