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- PDB-6uhw: Solution structure of an organic hydroperoxide resistance protein... -

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Basic information

Entry
Database: PDB / ID: 6uhw
TitleSolution structure of an organic hydroperoxide resistance protein from Burkholderia pseudomallei. Seattle Structural Genomics Center for Infectious Disease target BupsA.00074.a.
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / Melioidosis / infectious diseases / detoxification / biological warfare agent / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 speciesBurkholderia pseudomallei (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HHSN272201700059C United States
CitationJournal: Biomol.Nmr Assign. / Year: 2009
Title: Backbone and side chain (1)H, (13)C, and (15)N NMR assignments for the organic hydroperoxide resistance protein (Ohr) from Burkholderia pseudomallei.
Authors: Buchko, G.W. / Hewitt, S.N. / Napuli, A.J. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionSep 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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


Theoretical massNumber of molelcules
Total (without water)28,8262
Polymers28,8262
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Other data showed the protein was a dimer in solution. This included an estimation of the overall rotational correlation time, poor magnetization transfer in 3D NMR ...Evidence: gel filtration, Other data showed the protein was a dimer in solution. This included an estimation of the overall rotational correlation time, poor magnetization transfer in 3D NMR experiments with full protonated samples, and intermolecular NOE identification.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5580 Å2
ΔGint-40 kcal/mol
Surface area13700 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Organic hydroperoxide resistance protein


Mass: 14413.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: 1710b / Gene: ohr, BURPS1710b_A0863 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JK82

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
133isotropic12D 1H-15N HSQC
142isotropic23D C(CO)NH
152isotropic23D HN(CA)CB
1122isotropic43D (H)CCH-TOCSY
1111isotropic23D 1H-15N NOESY
1101isotropic23D 1H-13C NOESY aromatic
193isotropic13D 1H-13C NOESY aliphatic
181isotropic23D 1H-13C NOESY aliphatic
171isotropic43D HNCO
162isotropic43D HNCA
1133isotropic12D 1H-15N HSQC
1142isotropic43D H(CCO)NH
1154isotropic12D 1H-13C HSQC aliphatic
1161isotropic22D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] B74, 93% H2O/7% D2OB74_CN93% H2O/7% D2O
solution220 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM 99% 13C; U-99% 15N; 50%-2H]] B74, 93% H2O/7% D2OB74_CN50D93% H2O/7% D2O
solution320 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM 99% 13C; U-99% 15N] B74, 99% D2OB74_CN_D2O99% D2O
solution420 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM [U-10% 13C; U-99% 15N] B74, 93% H2O/7% D2OB74_10C93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTRISnatural abundance1
100 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
1 mMB74[U-99% 13C; U-99% 15N]1
20 mMTRISnatural abundance2
100 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
1 mMB7499% 13C; U-99% 15N; 50%-2H]]2
20 mMTRISnatural abundance3
100 mMsodium chloridenatural abundance3
1 mMDTTnatural abundance3
1 mMB7499% 13C; U-99% 15N]3
20 mMTRISnatural abundance4
100 mMsodium chloridenatural abundance4
1 mMDTTnatural abundance4
1 mMB74[U-10% 13C; U-99% 15N]4
Sample conditionsIonic strength: 0.12 M / Label: Cond1 / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II7501
Varian VXRSVarianVXRS7502
Varian VXRSVarianVXRS6004

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Processing

NMR software
NameVersionDeveloperClassification
Felix2007Accelrys Software Inc.processing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Sparky3.115Goddardchemical shift assignment
Sparky3.115Goddardpeak picking
Sparky3.115Goddarddata analysis
TALOS+Cornilescu, Delaglio and Baxdata analysis
PSVS1.5Bhattacharya and Montelionedata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 2
Details: Thirty-four pairs of intermolecular molecule distance restraints, identified with the assistance of homology models and confirmed in the NOE data, were introduced to coax the structure into ...Details: Thirty-four pairs of intermolecular molecule distance restraints, identified with the assistance of homology models and confirmed in the NOE data, were introduced to coax the structure into a dimeric structure using CYANA. STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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