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- PDB-5c04: Crystal structure of the F37H mutant AhpE from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 5c04
TitleCrystal structure of the F37H mutant AhpE from Mycobacterium tuberculosis
ComponentsPutative peroxiredoxin MT2298
KeywordsOXIDOREDUCTASE / 1-cys peroxiredoxin / peroxiredoxin / thioredoxin fold / Mycobacterium tuberculosis / active site mutant
Function / homology
Function and homology information


mycoredoxin-dependent peroxiredoxin / Tolerance by Mtb to nitric oxide produced by macrophages / response to nitrosative stress / thioredoxin peroxidase activity / peroxiredoxin 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsPallo, A. / Dufe, V.T. / Messens, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G.0305.12 Belgium
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: The active site architecture in peroxiredoxins: a case study on Mycobacterium tuberculosis AhpE.
Authors: Pedre, B. / van Bergen, L.A. / Pallo, A. / Rosado, L.A. / Dufe, V.T. / Molle, I.V. / Wahni, K. / Erdogan, H. / Alonso, M. / Proft, F.D. / Messens, J.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative peroxiredoxin MT2298
B: Putative peroxiredoxin MT2298


Theoretical massNumber of molelcules
Total (without water)33,6822
Polymers33,6822
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-13 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.300, 63.300, 159.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative peroxiredoxin MT2298 / Thioredoxin reductase / Alkylhydroperoxidase E


Mass: 16840.922 Da / Num. of mol.: 2 / Mutation: F37H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2298 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WIE2, UniProt: P9WIE3*PLUS, peroxiredoxin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium citrate tribasic, 0.1 M HEPES sodium, 30% v/v (+/-)-2-Methyl-2,4-pentanediol pH 7.5 mixed in 1:1 ratio with 30 mg/mL protein (in 20 mM HEPES sodium, 150 mM NaCl, pH 7.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.45→44.76 Å / Num. obs: 57365 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 30.077 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.077 / Χ2: 0.993 / Net I/σ(I): 18.54 / Num. measured all: 669845
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.45-1.490.6570.8861.8821860426034720.96381.5
1.49-1.530.7990.6762.7927912413037370.72590.5
1.53-1.570.9030.5234.0736425406939740.55497.7
1.57-1.620.9420.4265.6743289393739370.447100
1.62-1.670.9770.3198.0248174380538050.333100
1.67-1.730.9850.24710.448294369336920.258100
1.73-1.80.9910.1813.4245662357235700.18899.9
1.8-1.870.9950.14316.5745321346934690.149100
1.87-1.950.9950.11620.0442656329632960.121100
1.95-2.050.9960.09823.641793318031800.102100
2.05-2.160.9960.08726.2838396301130110.091100
2.16-2.290.9970.0828.9836937288528850.084100
2.29-2.450.9970.07631.5935575269926990.079100
2.45-2.640.9970.07232.4632354254625460.075100
2.64-2.90.9970.0734.5430283233623360.073100
2.9-3.240.9970.06735.8327136213421340.07100
3.24-3.740.9960.06636.5523796191719160.06999.9
3.74-4.580.9970.0653719910162416230.06899.9
4.58-6.480.9970.06536.6815683130313030.068100
6.480.9960.06934.6383897827800.07299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.55
Highest resolutionLowest resolution
Rotation44.76 Å1.89 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
REFMAC5.8.0073refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X0X

4x0x


Resolution: 1.45→44.76 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.1981 / WRfactor Rwork: 0.1773 / FOM work R set: 0.8646 / SU B: 2.443 / SU ML: 0.045 / SU R Cruickshank DPI: 0.059 / SU Rfree: 0.0634 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 1729 3 %RANDOM
Rwork0.1657 ---
obs0.1667 55523 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.54 Å2 / Biso mean: 27.638 Å2 / Biso min: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.55 Å2
Refinement stepCycle: final / Resolution: 1.45→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 0 167 2545
Biso mean---33.85 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192529
X-RAY DIFFRACTIONr_bond_other_d0.0010.022384
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9363465
X-RAY DIFFRACTIONr_angle_other_deg0.79835469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01823.968126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27615392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9881519
X-RAY DIFFRACTIONr_chiral_restr0.090.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02636
X-RAY DIFFRACTIONr_mcbond_it1.181.7421256
X-RAY DIFFRACTIONr_mcbond_other1.1711.741255
X-RAY DIFFRACTIONr_mcangle_it1.8092.6061576
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 114 -
Rwork0.298 3432 -
all-3546 -
obs--83.59 %
Refinement TLS params.Method: refined / Origin x: -17.8255 Å / Origin y: 23.2412 Å / Origin z: 0.5165 Å
111213212223313233
T0.0305 Å20.0315 Å20.0067 Å2-0.07 Å20.0379 Å2--0.0363 Å2
L0.7603 °2-0.2194 °20.4575 °2-0.485 °2-0.7065 °2--1.6571 °2
S-0.002 Å °-0.0484 Å °-0.0787 Å °-0.1025 Å °-0.1163 Å °-0.0308 Å °0.1001 Å °0.1686 Å °0.1183 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 152
2X-RAY DIFFRACTION1B1 - 152

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