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- PDB-6ebg: Ohr (Organic Hydroperoxide Resistance protein) mutant - C60S inte... -

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Basic information

Entry
Database: PDB / ID: 6ebg
TitleOhr (Organic Hydroperoxide Resistance protein) mutant - C60S interacting with dihydrolipoamide
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / Ohr / thiol-proxidase / dihydrolipoamide
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
(6S)-6,8-disulfanyloctanamide / Organic hydroperoxide resistance protein / Organic hydroperoxide resistance protein
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 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)68,1778
Polymers67,3474
Non-polymers8294
Water1,27971
1
A: Organic hydroperoxide resistance protein
B: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0884
Polymers33,6742
Non-polymers4152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-43 kcal/mol
Surface area12950 Å2
MethodPISA
2
C: Organic hydroperoxide resistance protein
D: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0884
Polymers33,6742
Non-polymers4152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-44 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.646, 88.646, 180.107
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
15METMETALAALABB1 - 14121 - 161
25METMETALAALADD1 - 14121 - 161
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: 16836.842 Da / Num. of mol.: 4 / Mutation: C60S
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-J3S / (6S)-6,8-disulfanyloctanamide


Mass: 207.357 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H17NOS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: Purified Ohr_C60S protein 10mg/ml in 5mM Tris-Hcl pH 7.4 Crystallisation conditions: Magnesium Clhoride 200mM, BIS-TRIS 100mM pH 5.5, PEG 3,350 25%w/v crystal was soaked overnight in ...Details: Purified Ohr_C60S protein 10mg/ml in 5mM Tris-Hcl pH 7.4 Crystallisation conditions: Magnesium Clhoride 200mM, BIS-TRIS 100mM pH 5.5, PEG 3,350 25%w/v crystal was soaked overnight in Lipoamide 5mM, solved in 5% ethanol and Crystallisation condition

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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
RadiationMonochromator: 0.97946 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→39.8 Å / Num. obs: 40280 / % possible obs: 92.5 % / Redundancy: 19.8 % / CC1/2: 0.999 / Rpim(I) all: 0.07 / Rrim(I) all: 0.227 / Net I/σ(I): 14.1
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 17.9 % / Num. unique obs: 3786 / CC1/2: 0.463 / Rpim(I) all: 1.913 / Rrim(I) all: 5.789 / % possible all: 99.9

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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: 2.15→39.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 16.723 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23595 1934 4.8 %RANDOM
Rwork0.2005 ---
obs0.20227 38284 92.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.961 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å2-0 Å2
2--0.75 Å2-0 Å2
3----2.45 Å2
Refinement stepCycle: 1 / Resolution: 2.15→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4096 0 48 71 4215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174002
X-RAY DIFFRACTIONr_angle_refined_deg1.781.6455656
X-RAY DIFFRACTIONr_angle_other_deg1.3711.5739274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5095558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24621.2200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56715682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3381536
X-RAY DIFFRACTIONr_chiral_restr0.0770.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
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_it2.0463.072244
X-RAY DIFFRACTIONr_mcbond_other2.0463.072243
X-RAY DIFFRACTIONr_mcangle_it3.2544.5972798
X-RAY DIFFRACTIONr_mcangle_other3.2544.5972799
X-RAY DIFFRACTIONr_scbond_it2.4233.4711948
X-RAY DIFFRACTIONr_scbond_other2.4233.4721949
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8725.0392859
X-RAY DIFFRACTIONr_long_range_B_refined5.58535.9264178
X-RAY DIFFRACTIONr_long_range_B_other5.57735.8794172
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)
11A36110.09
12B36110.09
21A36860.08
22C36860.08
31A36140.09
32D36140.09
41B36420.09
42C36420.09
51B37720.08
52D37720.08
61C36540.1
62D36540.1
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 155 -
Rwork0.371 3080 -
obs--99.88 %
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)
11.71180.3216-0.26144.37190.33353.00460.06910.17790.1064-0.37870.0547-0.0565-0.06910.0321-0.12380.2261-0.03240.05090.1929-0.00570.019736.8925-3.91931.6794
22.92860.70440.31924.03250.3342.0897-0.00020.08810.2869-0.03010.1097-0.2477-0.19810.0768-0.10950.2197-0.05270.04110.1952-0.01020.064839.92373.878111.4347
32.5613-1.1095-0.27535.2427-0.58752.8517-0.0213-0.26620.14170.85110.16940.0328-0.18170.024-0.14810.37330.06130.03720.2010.00490.017852.7658-9.6507-25.011
42.9291-0.97860.27344.34510.03882.03910.00820.04010.2190.27890.11850.3519-0.25630.0509-0.12660.27880.03670.06810.18470.03120.076748.5865-2.4796-34.7531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 141
2X-RAY DIFFRACTION2B1 - 141
3X-RAY DIFFRACTION3C2 - 141
4X-RAY DIFFRACTION4D1 - 141

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