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- PDB-1usp: Organic Hydroperoxide Resistance Protein from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 1usp
TitleOrganic Hydroperoxide Resistance Protein from Deinococcus radiodurans
Components(ORGANIC HYDROPEROXIDE RESISTANCE PROTEIN) x 2
KeywordsOXIDOREDUCTASE / 2-CYS PEROXIDASE
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 speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMeunier-Jamin, C. / Kapp, U. / Leonard, G. / McSweeney, S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Structure of the Organic Hydroperoxide Resistance Protein from Deinococcus Radiodurans: Do Conformational Changes Facilitate Recycling of the Redox Disulfide?
Authors: Meunier-Jamin, C. / Kapp, U. / Leonard, G. / Mcsweeney, S.
History
DepositionNov 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8207
Polymers29,3602
Non-polymers4605
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.408, 56.600, 49.458
Angle α, β, γ (deg.)90.00, 90.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.816, -0.565, 0.122), (-0.563, 0.729, -0.389), (0.131, -0.386, -0.913)
Vector: 49.027, 22.631, 29.783)

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Components

#1: Protein ORGANIC HYDROPEROXIDE RESISTANCE PROTEIN


Mass: 14686.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RTA8
#2: Protein ORGANIC HYDROPEROXIDE RESISTANCE PROTEIN


Mass: 14672.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RTA8
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.2 Å3/Da / Density % sol: 42 %
Crystal growpH: 7.2 / Details: pH 7.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→49.4 Å / Num. obs: 18043 / % possible obs: 91 % / Redundancy: 3.1 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.4 / % possible all: 62.5

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.4 Å / SU B: 3.5 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.14
Details: IN BOTH MOLECULES MAKING UP THE HOMODIMER, ARG15 HAS BEEN AND MODELLED AS ALA, ALA16 AS GLY AND THE SIDE-CHAINS OF LYS70 GLU108 IN BOTH MOLECULES HAVE BEEN TRUNCATED AT THE CG ATOM. ...Details: IN BOTH MOLECULES MAKING UP THE HOMODIMER, ARG15 HAS BEEN AND MODELLED AS ALA, ALA16 AS GLY AND THE SIDE-CHAINS OF LYS70 GLU108 IN BOTH MOLECULES HAVE BEEN TRUNCATED AT THE CG ATOM. ADDITIONALLY, THE SIDE-CHAINS OF ILE71A, ASP76A, GLU139A AND LYS87B HAVE BEEN TRUNCATED AT CB. ILE71B HAS BEEN TRUNCATED AT CG2, ARG107B AT CG. GLU69B HAS BEEN MODELLED AS ASN
RfactorNum. reflection% reflectionSelection details
Rfree0.204 921 5.1 %RANDOM
Rwork0.171 ---
obs0.173 18043 91 %-
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å20 Å2-0.13 Å2
2---1.8 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 30 123 2100

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