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- PDB-1qwi: Crystal Structure of E. coli OsmC -

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Basic information

Entry
Database: PDB / ID: 1qwi
TitleCrystal Structure of E. coli OsmC
Componentsosmotically inducible protein
Keywordshydroperoxide reductase / hydroperoxide resistance
Function / homology
Function and homology information


peroxiredoxin activity / hyperosmotic response / response to hydroperoxide / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / response to oxidative stress / protein homodimerization activity / cytosol
Similarity search - Function
Peroxiredoxin OsmC / : / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsLesniak, J. / Barton, W.A. / Nikolov, D.B.
CitationJournal: Protein Sci. / Year: 2003
Title: Structural and functional features of the Escherichia coli hydroperoxide resistance protein OsmC
Authors: Lesniak, J. / Barton, W.A. / Nikolov, D.B.
History
DepositionSep 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: osmotically inducible protein
B: osmotically inducible protein
C: osmotically inducible protein
D: osmotically inducible protein


Theoretical massNumber of molelcules
Total (without water)61,1034
Polymers61,1034
Non-polymers00
Water9,080504
1
A: osmotically inducible protein
B: osmotically inducible protein


Theoretical massNumber of molelcules
Total (without water)30,5522
Polymers30,5522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-39 kcal/mol
Surface area11800 Å2
MethodPISA
2
C: osmotically inducible protein
D: osmotically inducible protein


Theoretical massNumber of molelcules
Total (without water)30,5522
Polymers30,5522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-39 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.747, 64.229, 67.585
Angle α, β, γ (deg.)90.00, 92.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
osmotically inducible protein / osmc


Mass: 15275.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 0157:H7 EDL399 / Gene: OsmC / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0L2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 5000 MME, 0.2M Ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
25 mMTris1droppH8.0
35 mMdithiothreitol1drop
40.2 Mammonium sulfate1reservoir
530 %PEG5000 MME1reservoir
60.1 MMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9795, 0.9793, 0.9770
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.9771
ReflectionResolution: 1.8→30 Å / Num. all: 51960 / Num. obs: 48947 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053 / Rsym value: 0.045
Reflection shellResolution: 1.8→1.88 Å / % possible all: 94.8
Reflection
*PLUS
% possible obs: 99.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.09 Å / % possible obs: 98.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Freidel pairs were used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 4810 -random
Rwork0.2221 ---
all-102329 --
obs-98304 96 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 0 504 4656
Refinement
*PLUS
Lowest resolution: 500 Å / Num. reflection obs: 93520 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.006
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.36
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.09 Å

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