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- PDB-1xvw: Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cy... -

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Basic information

Entry
Database: PDB / ID: 1xvw
TitleCrystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin
ComponentsHypothetical protein Rv2238c/MT2298Hypothesis
KeywordsOXIDOREDUCTASE / thioredoxin fold / Oxidized cystein sulfenic acid / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


mycoredoxin-dependent peroxiredoxin / Tolerance by Mtb to nitric oxide produced by macrophages / response to nitrosative stress / peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis / peroxidase activity / cellular response to oxidative stress / cytosol / cytoplasm
Similarity search - Function
Peroxiredoxin, AhpC-type / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkyl hydroperoxide reductase E / Alkyl hydroperoxide reductase E
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsLi, S. / Peterson, N.A. / Kim, M.Y. / Kim, C.Y. / Hung, L.W. / Yu, M. / Lekin, T. / Segelke, B.W. / Lott, J.S. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys Peroxiredoxin
Authors: Li, S. / Peterson, N.A. / Kim, M.Y. / Kim, C.Y. / Hung, L.W. / Yu, M. / Lekin, T. / Segelke, B.W. / Lott, J.S. / Baker, E.N.
History
DepositionOct 28, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein Rv2238c/MT2298
B: Hypothetical protein Rv2238c/MT2298


Theoretical massNumber of molelcules
Total (without water)35,2302
Polymers35,2302
Non-polymers00
Water3,315184
1
A: Hypothetical protein Rv2238c/MT2298
B: Hypothetical protein Rv2238c/MT2298

A: Hypothetical protein Rv2238c/MT2298
B: Hypothetical protein Rv2238c/MT2298

A: Hypothetical protein Rv2238c/MT2298
B: Hypothetical protein Rv2238c/MT2298

A: Hypothetical protein Rv2238c/MT2298
B: Hypothetical protein Rv2238c/MT2298


Theoretical massNumber of molelcules
Total (without water)140,9198
Polymers140,9198
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Unit cell
Length a, b, c (Å)147.994, 147.994, 33.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a octamer generated from the dimer in the asymmetric unit by the crystallographic 4-fold symmetry

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Components

#1: Protein Hypothetical protein Rv2238c/MT2298 / Hypothesis / 1-cys alkylhydroperoxiredoxin reductase


Mass: 17614.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rv2238c / Plasmid: pProEX HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P65688, UniProt: P9WIE3*PLUS, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 4.61 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.8M sodium malonate pH 5.0, 0.1M sodium acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00000, 0.97937, 0.97918, 0.95370
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979371
30.979181
40.95371
ReflectionResolution: 1.87→46.8 Å / Num. obs: 33679 / Redundancy: 97.6 % / Biso Wilson estimate: 17.4 Å2 / Net I/σ(I): 17.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 80.7 % / Mean I/σ(I) obs: 1.58 / Num. unique all: 2764

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→46.8 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1828 -RANDOM
Rwork0.18 ---
all-30763 --
obs-30635 99.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2---2.29 Å20 Å2
3---4.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 0 184 2662
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it0.012
X-RAY DIFFRACTIONc_mcangle_it1.58
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.87-1.960.2962100.2520.02348898.1
1.96-2.060.2522370.2030.016376698.8
2.06-2.190.2412240.1880.016377999.4
2.19-2.360.1932310.1650.013382399.5
2.36-2.590.2292430.1750.015386099.8
2.59-2.970.2242230.1770.015382499.8

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