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- PDB-1n2f: CRYSTAL STRUCTURE OF P. AERUGINOSA OHR -

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Basic information

Entry
Database: PDB / ID: 1n2f
TitleCRYSTAL STRUCTURE OF P. AERUGINOSA OHR
ComponentsOrganic Hydroperoxide Resistance Protein
KeywordsOXIDOREDUCTASE / Peroxide reductase
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Organic hydroperoxide resistance protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsLesniak, J. / Barton, W.A. / Nikolov, D.B.
CitationJournal: Embo J. / Year: 2002
Title: Structural and functional characterization of the Pseudomonas hydroperoxide resistance protein Ohr
Authors: Lesniak, J. / Barton, W.A. / Nikolov, D.B.
History
DepositionOct 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Author states the ohr protein that was solved was engineered to have three methionines in ...SEQUENCE Author states the ohr protein that was solved was engineered to have three methionines in place of leucines, which allowed the authors to use selenomethionine for phasing in the experiment. Furthermore, the author states the engineered mutations are not present in the wild type protein.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4904
Polymers29,1812
Non-polymers3092
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-59 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.911, 77.510, 43.079
Angle α, β, γ (deg.)90.00, 116.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Organic Hydroperoxide Resistance Protein


Mass: 14590.513 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: ohr / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HZZ3
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
25 mMTris1droppH8.0
35 mMdithiothreitol1drop
40.2 Msodium acetate1reservoir
530 %PEG5000 MME1reservoir
60.1 MTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979,0.979,0.961
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2002
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9611
ReflectionResolution: 2→30 Å / Num. all: 30862 / Num. obs: 29936 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.9 Å2
Reflection shellResolution: 2→2.09 Å / % possible all: 96.5
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % possible obs: 97.9 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.053

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.01→19.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 377931.62 / Data cutoff high rms absF: 377931.62 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2848 9.6 %RANDOM
Rwork0.22 ---
all0.23 29679 --
obs0.22 29679 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4685 Å2 / ksol: 0.455286 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å21.19 Å2
2--0.54 Å20 Å2
3---1.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.01→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 16 170 2220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.01→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 460 10.6 %
Rwork0.254 3866 -
obs-29679 83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.PARAM
X-RAY DIFFRACTION3DTT.PARDTT.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Rfactor obs: 0.22 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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