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- PDB-7bz6: Mycobacterium bovis AhpC -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7bz6
TitleMycobacterium bovis AhpC
ComponentsAlkyl hydroperoxide reductase C peptide
KeywordsOXIDOREDUCTASE / ALKYL HYDROPEROXIDASE C
Function / homology
Function and homology information


peroxiredoxin activity / peroxidase activity / response to oxidative stress / cytoplasm
Similarity search - Function
Alkyl hydroperoxide reductase subunit C / Peroxiredoxin, AhpC-type / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Alkyl hydroperoxide reductase C
Similarity search - Component
Biological speciesMycobacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.302 Å
AuthorsChong, S.M.S. / Neelagandan, K. / Gruber, G.
CitationJournal: Febs Lett. / Year: 2020
Title: Residues of helix alpha2 are critical for catalytic efficiency of mycobacterial alkylhydroperoxide reductase subunit C.
Authors: Chong, S.M.S. / Kamariah, N. / Gruber, G.
History
DepositionApr 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase C peptide
B: Alkyl hydroperoxide reductase C peptide


Theoretical massNumber of molelcules
Total (without water)44,8862
Polymers44,8862
Non-polymers00
Water00
1
A: Alkyl hydroperoxide reductase C peptide
B: Alkyl hydroperoxide reductase C peptide
x 6


Theoretical massNumber of molelcules
Total (without water)269,31612
Polymers269,31612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Unit cell
Length a, b, c (Å)137.554, 137.554, 96.842
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 or resid 4 through 23...
21(chain B and (resid 2 or resid 4 through 23...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPRO(chain A and (resid 2 or resid 4 through 23...AA28
12LEULEULEULEU(chain A and (resid 2 or resid 4 through 23...AA4 - 2310 - 29
13SERSERGLNGLN(chain A and (resid 2 or resid 4 through 23...AA24 - 3030 - 36
14METMETSERSER(chain A and (resid 2 or resid 4 through 23...AA1 - 1707 - 176
15METMETSERSER(chain A and (resid 2 or resid 4 through 23...AA1 - 1707 - 176
16METMETSERSER(chain A and (resid 2 or resid 4 through 23...AA1 - 1707 - 176
17METMETSERSER(chain A and (resid 2 or resid 4 through 23...AA1 - 1707 - 176
21PROPROPROPRO(chain B and (resid 2 or resid 4 through 23...BB28
22LEULEULEULEU(chain B and (resid 2 or resid 4 through 23...BB4 - 2310 - 29
23SERSERGLNGLN(chain B and (resid 2 or resid 4 through 23...BB24 - 3030 - 36
24METMETARGARG(chain B and (resid 2 or resid 4 through 23...BB1 - 1797 - 185
25METMETARGARG(chain B and (resid 2 or resid 4 through 23...BB1 - 1797 - 185
26METMETARGARG(chain B and (resid 2 or resid 4 through 23...BB1 - 1797 - 185
27METMETARGARG(chain B and (resid 2 or resid 4 through 23...BB1 - 1797 - 185

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Components

#1: Protein Alkyl hydroperoxide reductase C peptide


Mass: 22443.010 Da / Num. of mol.: 2 / Mutation: A67D, C176S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (bacteria) / Gene: ahpC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q79CV0

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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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 0.1 M sodium citrate, 16% ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 8387 / % possible obs: 98 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.018 / Rrim(I) all: 0.085 / Χ2: 0.823 / Net I/σ(I): 10.6
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.589 / Num. unique obs: 727 / CC1/2: 0.896 / Rpim(I) all: 0.211 / Rrim(I) all: 0.63 / Χ2: 0.712 / % possible all: 88.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BMX

2bmx


Resolution: 3.302→33.039 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 43.76
RfactorNum. reflection% reflection
Rfree0.344 391 4.79 %
Rwork0.309 --
obs0.311 8164 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 529.94 Å2 / Biso min: 73.55 Å2
Refinement stepCycle: final / Resolution: 3.302→33.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 0 0 2753
Num. residues----349
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1405X-RAY DIFFRACTION16.784TORSIONAL
12B1405X-RAY DIFFRACTION16.784TORSIONAL
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)
13.385-0.2345-0.76762.78780.111.9934-0.1687-0.0290.3675-0.3191-0.53780.1819-1.55750.00330.03022.7242-0.022-1.39830.91130.00831.944270.1613170.957715.5444
22.9114-0.3907-1.98512.3822-0.87621.52690.0874-0.5498-0.0620.5505-0.236-0.5236-0.93260.41610.262.0563-0.7351-1.25131.4310.5592.043294.2995164.209432.2004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' )
2X-RAY DIFFRACTION2(chain 'B' )

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