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- PDB-4xih: Crystal structure of the R116A mutant AhpE from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 4xih
TitleCrystal structure of the R116A mutant AhpE from Mycobacterium tuberculosis
ComponentsAhpC/TSA family protein
KeywordsOXIDOREDUCTASE / Peroxiredoxins
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
AhpC/TSA family protein / Alkyl hydroperoxide reductase E
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsTamu Dufe, V. / van Molle, I. / Pallo, A. / Messens, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G030512N 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
DepositionJan 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Aug 24, 2016Group: Database references
Revision 2.0Mar 25, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AhpC/TSA family protein
B: AhpC/TSA family protein


Theoretical massNumber of molelcules
Total (without water)33,6302
Polymers33,6302
Non-polymers00
Water1,08160
1
A: AhpC/TSA family protein

B: AhpC/TSA family protein


Theoretical massNumber of molelcules
Total (without water)33,6302
Polymers33,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_564-x+1/2,-y+3/2,z-1/21
Buried area1450 Å2
ΔGint-13 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.260, 147.260, 33.303
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein AhpC/TSA family protein / Peroxiredoxin AhpE


Mass: 16814.902 Da / Num. of mol.: 2 / Mutation: R116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CCDC5079) (bacteria)
Gene: ahpE, CCDC5079_2075, CFBS_2371 / Production host: Escherichia coli (E. coli) / References: UniProt: F7WEJ6, UniProt: P9WIE3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M Na-malonate, 0.1 M Na-acetate, pH 4.5 / PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.25→104 Å / Num. obs: 17069 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 2.73 % / Biso Wilson estimate: 45.05 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.111 / Χ2: 1.009 / Net I/σ(I): 10.93 / Num. measured all: 74903
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
2.25-2.310.70.8161.834291127011050.93287
2.31-2.370.7190.7072.395328125912190.80296.8
2.37-2.440.8010.6022.785141119311760.68498.6
2.44-2.510.8240.5743.045439119511820.64898.9
2.51-2.590.8710.4613.844932111211030.52299.2
2.59-2.690.9150.3564.774923112211120.40499.1
2.69-2.790.9390.2855.914888108210650.32198.4
2.79-2.90.9640.2067.644420101510000.23498.5
2.9-3.030.9690.1758.81436610169960.298
3.03-3.180.9740.13811.9142189239160.15899.2
3.18-3.350.9850.10614.4541689099080.1299.9
3.35-3.550.990.08117.4636548408340.09299.3
3.55-3.80.9940.06620.2336368158010.07698.3
3.8-4.10.9950.05821.7832307557430.06698.4
4.1-4.490.9960.04824.2828276996830.05597.7
4.49-5.030.9960.04924.8126936386330.05699.2
5.03-5.80.9970.0522.4823565695600.05798.4
5.8-7.110.9960.05123.4820244764680.05798.3
7.11-10.050.9980.03927.4715293813640.04495.5
10.050.9980.03528.248402332010.03986.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.4 Å36.81 Å
Translation6.4 Å36.81 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X0X

4x0x


Resolution: 2.25→104 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2122 / WRfactor Rwork: 0.1927 / FOM work R set: 0.8058 / SU B: 14.934 / SU ML: 0.175 / SU R Cruickshank DPI: 0.3025 / SU Rfree: 0.2022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 962 5.6 %RANDOM
Rwork0.2095 16096 --
obs0.2104 16096 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.87 Å2 / Biso mean: 40.799 Å2 / Biso min: 17.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 2.25→104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 0 60 2436
Biso mean---38.13 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192458
X-RAY DIFFRACTIONr_bond_other_d0.0010.022297
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9333351
X-RAY DIFFRACTIONr_angle_other_deg0.7235257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6745310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.29623.884121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.05815367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.551517
X-RAY DIFFRACTIONr_chiral_restr0.0740.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212865
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02616
X-RAY DIFFRACTIONr_mcbond_it0.9273.2451231
X-RAY DIFFRACTIONr_mcbond_other0.9273.2441230
X-RAY DIFFRACTIONr_mcangle_it1.7044.8651538
LS refinement shellResolution: 2.25→2.309 Å
RfactorNum. reflection% reflection
Rfree0.303 54 -
Rwork0.256 1100 -
obs--91.08 %
Refinement TLS params.Method: refined / Origin x: 24.5177 Å / Origin y: 121.1007 Å / Origin z: -35.7148 Å
111213212223313233
T0.0615 Å20.0022 Å20.0178 Å2-0.0637 Å2-0.0249 Å2--0.0332 Å2
L0.5903 °20.4783 °2-0.1123 °2-0.6289 °20.0719 °2--0.5138 °2
S0.0908 Å °-0.0427 Å °0.0672 Å °-0.0302 Å °-0.022 Å °0.0229 Å °-0.0897 Å °-0.0537 Å °-0.0688 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 152
2X-RAY DIFFRACTION1B1 - 152

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