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- PDB-6eb4: OhrB (Organic Hydroperoxide Resistance protein) from Chromobacter... -

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Basic information

Entry
Database: PDB / ID: 6eb4
TitleOhrB (Organic Hydroperoxide Resistance protein) 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
DI(HYDROXYETHYL)ETHER / Organic hydroperoxide resistance protein / Organic hydroperoxide resistance protein
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 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)67,8368
Polymers67,4124
Non-polymers4244
Water2,864159
1
A: Organic hydroperoxide resistance protein
B: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9184
Polymers33,7062
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-36 kcal/mol
Surface area12500 Å2
MethodPISA
2
C: Organic hydroperoxide resistance protein
D: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9184
Polymers33,7062
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-35 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.269, 87.269, 178.779
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: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA2 - 14022 - 160
21LEULEUBB2 - 14022 - 160
12LEULEUAA2 - 14022 - 160
22LEULEUCC2 - 14022 - 160
13LEULEUAA2 - 14022 - 160
23LEULEUDD2 - 14022 - 160
14ALAALABB2 - 14122 - 161
24ALAALACC2 - 14122 - 161
15ALAALABB2 - 14122 - 161
25ALAALADD2 - 14122 - 161
16ALAALACC2 - 14122 - 161
26ALAALADD2 - 14122 - 161

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, UniProt: Q7NV52*PLUS
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.92 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Purified protein at 10mg/ml diluted in 5mM Tris-Hcl pH 7.4 Crystallisation condition: Magnesium Clhoride 200mM, BIS-TRIS 100mM pH 5.5, PEG 3,350 25%w/v

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.45866 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45866 Å / Relative weight: 1
ReflectionResolution: 2.1→46.8 Å / Num. obs: 43780 / % possible obs: 97.5 % / Redundancy: 14.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 22.5
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 8.5 % / Rmerge(I) obs: 2.61 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3282 / CC1/2: 0.37 / Rpim(I) all: 1.16 / Rrim(I) all: 2.46 / % possible all: 89.3

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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: 2.1→35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 11.009 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22033 2294 5.2 %RANDOM
Rwork0.19188 ---
obs0.19338 41419 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.888 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å2-0 Å2
3----3.32 Å2
Refinement stepCycle: 1 / Resolution: 2.1→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 28 159 4275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134167
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173965
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.6415624
X-RAY DIFFRACTIONr_angle_other_deg1.4041.5729181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3515557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46421.2200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30615679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8051536
X-RAY DIFFRACTIONr_chiral_restr0.0770.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
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_it2.1813.5012240
X-RAY DIFFRACTIONr_mcbond_other2.1793.5012239
X-RAY DIFFRACTIONr_mcangle_it3.3195.2422793
X-RAY DIFFRACTIONr_mcangle_other3.3185.2432794
X-RAY DIFFRACTIONr_scbond_it2.8463.8851927
X-RAY DIFFRACTIONr_scbond_other2.8463.8851928
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2885.662832
X-RAY DIFFRACTIONr_long_range_B_refined6.25542.0624383
X-RAY DIFFRACTIONr_long_range_B_other6.23241.8464350
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)
11A36580.12
12B36580.12
21A38220.08
22C38220.08
31A36840.12
32D36840.12
41B36530.12
42C36530.12
51B37430.11
52D37430.11
61C37070.12
62D37070.12
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 146 -
Rwork0.347 2805 -
obs--89.13 %
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)
13.00940.8748-0.21653.8723-0.55112.17120.0918-0.01460.31070.16090.0334-0.09-0.17410.1496-0.12520.0916-0.04690.03410.0303-0.02390.0555114.3432111.75460.6233
23.80811.4158-0.48022.5390.23453.69470.1637-0.3710.09440.2692-0.045-0.0433-0.10580.1399-0.11870.1033-0.04820.03720.0639-0.03590.0283109.1863105.242610.2945
32.32081.0535-0.09934.9685-0.21272.15-0.05690.0015-0.0765-0.42480.25040.39660.34760.0209-0.19350.1596-0.0716-0.09240.0550.04250.070191.113478.238-12.7857
42.6151.30180.48786.1052-0.86113.2666-0.09140.2677-0.0624-1.09450.28020.03050.30560.0433-0.18890.3198-0.108-0.05540.07740.01940.025595.282685.2343-22.634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 141
2X-RAY DIFFRACTION2B2 - 141
3X-RAY DIFFRACTION3C2 - 141
4X-RAY DIFFRACTION4D2 - 141

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