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- PDB-2bmx: Mycobacterium tuberculosis AhpC -

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Basic information

Entry
Database: PDB / ID: 2bmx
TitleMycobacterium tuberculosis AhpC
ComponentsALKYL HYDROPEROXIDASE C
KeywordsOXIDOREDUCTASE / PEROXIREDOXIN / ANTIOXIDANT DEFENSE SYSTEM / MYCOBACTERIUM TUBERCULOSIS / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


lipoyl-dependent peroxiredoxin / hydroperoxide reductase activity / Cell redox homeostasis / Tolerance of reactive oxygen produced by macrophages / Tolerance by Mtb to nitric oxide produced by macrophages / NADH-dependent peroxiredoxin activity / response to nitrosative stress / peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis ...lipoyl-dependent peroxiredoxin / hydroperoxide reductase activity / Cell redox homeostasis / Tolerance of reactive oxygen produced by macrophages / Tolerance by Mtb to nitric oxide produced by macrophages / NADH-dependent peroxiredoxin activity / response to nitrosative stress / peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis / peptidoglycan-based cell wall / hydrogen peroxide catabolic process / peroxidase activity / response to oxidative stress / oxidoreductase activity / plasma membrane / cytoplasm / cytosol
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 C / Alkyl hydroperoxide reductase C
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsGuimaraes, B.G. / Alzari, P.M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure and Mechanism of the Alkyl Hydroperoxidase Ahpc, a Key Element of the Mycobacterium Tuberculosis Defense System Against Oxidative Stress.
Authors: Guimaraes, B.G. / Souchon, H. / Honore, N. / Saint-Joanis, B. / Brosch, R. / Shepard, W. / Cole, S.T. / Alzari, P.M.
History
DepositionMar 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALKYL HYDROPEROXIDASE C
B: ALKYL HYDROPEROXIDASE C
C: ALKYL HYDROPEROXIDASE C


Theoretical massNumber of molelcules
Total (without water)64,9923
Polymers64,9923
Non-polymers00
Water5,116284
1
A: ALKYL HYDROPEROXIDASE C
B: ALKYL HYDROPEROXIDASE C
x 6


Theoretical massNumber of molelcules
Total (without water)259,96712
Polymers259,96712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
MethodPQS
2
C: ALKYL HYDROPEROXIDASE C
x 12


Theoretical massNumber of molelcules
Total (without water)259,96712
Polymers259,96712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation12_556x,x-y,-z+11
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation11_556-x+y,y,-z+11
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation9_556-x,-x+y,-z+11
crystal symmetry operation10_556-y,-x,-z+11
crystal symmetry operation4_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)139.265, 139.265, 148.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein ALKYL HYDROPEROXIDASE C / ALKYL HYDROPEROXIDE REDUCTASE C / PROTEIN AHPC


Mass: 21663.902 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q7BHK8, UniProt: P9WQB7*PLUS, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 176 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 176 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 176 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 176 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 176 TO SER
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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 7 / Details: 0.1 M NA CITRATE, PH 6.0, 16% AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 33798 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 31.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 31.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→141.42 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.231 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1712 5.1 %RANDOM
Rwork0.195 ---
obs0.197 32082 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.4→141.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3963 0 0 284 4247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.9355549
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5865513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69424.518197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.78315582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.061522
X-RAY DIFFRACTIONr_chiral_restr0.1470.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023177
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21843
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22740
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3620.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0371.52628
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59424128
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.48831622
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8394.51421
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 132
Rwork0.228 2311
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.7546-0.3147-0.76961.08210.0542.30840.03230.49030.7555-0.0606-0.01760.0322-0.414-0.0455-0.0146-0.078-0.012-0.015-0.07230.054-0.12461.904151.577415.5708
24.4609-2.0826-0.60382.88810.61432.2857-0.0583-0.00380.5942-0.00790.1189-0.5011-0.30710.2864-0.0605-0.1106-0.04-0.0107-0.14810.0011-0.124925.762344.868131.7098
32.6251-2.2549-0.5473.91451.29313.0232-0.0683-0.05580.32320.12190.2153-0.7094-0.23720.446-0.1469-0.1437-0.0082-0.0147-0.1313-0.018-0.114236.104936.516882.3453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 170
2X-RAY DIFFRACTION2B1 - 179
3X-RAY DIFFRACTION3C1 - 170

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