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- PDB-8dwr: Crystal structure of the L333V variant of catalase-peroxidase fro... -

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Basic information

Entry
Database: PDB / ID: 8dwr
TitleCrystal structure of the L333V variant of catalase-peroxidase from Mycobacterium tuberculosis
ComponentsCatalase-peroxidase
KeywordsOXIDOREDUCTASE / Catalase-peroxidase / KatG / Heme
Function / homology
Function and homology information


oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / NADH binding / catalase activity / NADPH binding / peptidoglycan-based cell wall / positive regulation of DNA repair / hydrogen peroxide catabolic process / peroxidase activity ...oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / NADH binding / catalase activity / NADPH binding / peptidoglycan-based cell wall / positive regulation of DNA repair / hydrogen peroxide catabolic process / peroxidase activity / cellular response to hydrogen peroxide / response to oxidative stress / response to antibiotic / heme binding / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Catalase-peroxidase haem / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / TRIETHYLENE GLYCOL / Catalase-peroxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDiaz-Vilchis, A. / Uribe-Vazquez, B. / Avila-Linares, A. / Rudino-Pinera, E. / Soberon, X.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Other governmentIBt, UNAM Institutional budget Mexico
CitationJournal: Biochem Biophys Rep / Year: 2024
Title: Characterization of a catalase-peroxidase variant (L333V-KatG) identified in an INH-resistant Mycobacterium tuberculosis clinical isolate.
Authors: Uribe-Vazquez, B. / Diaz-Vilchis, A. / Avila-Linares, A. / Saab-Rincon, G. / Marin-Tovar, Y. / Flores, H. / Pastor, N. / Huerta-Miranda, G. / Rudino-Pinera, E. / Soberon, X.
History
DepositionAug 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catalase-peroxidase
B: Catalase-peroxidase
C: Catalase-peroxidase
D: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,25020
Polymers326,1384
Non-polymers4,11216
Water39,5072193
1
A: Catalase-peroxidase
B: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,12510
Polymers163,0692
Non-polymers2,0568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14150 Å2
ΔGint-117 kcal/mol
Surface area49520 Å2
MethodPISA
2
C: Catalase-peroxidase
D: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,12510
Polymers163,0692
Non-polymers2,0568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-114 kcal/mol
Surface area49830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.671, 150.817, 127.037
Angle α, β, γ (deg.)90.000, 90.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Catalase-peroxidase / CP / Peroxidase/catalase


Mass: 81534.477 Da / Num. of mol.: 4 / Mutation: L333V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: katG, Rv1908c, MTCY180.10 / Plasmid: pKK-KatG / Production host: Escherichia coli (E. coli) / References: UniProt: P9WIE5, catalase-peroxidase

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Non-polymers , 5 types, 2209 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2193 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10 % w/v PEG 6000 100 mM HEPES / Sodium Hydroxide; pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 178934 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 8861 / CC1/2: 0.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CCA

2cca


Resolution: 2.1→19.992 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 2007 1.12 %
Rwork0.1808 176855 -
obs0.1813 178862 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.3 Å2 / Biso mean: 24.566 Å2 / Biso min: 4.54 Å2
Refinement stepCycle: final / Resolution: 2.1→19.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22124 0 276 2195 24595
Biso mean--24.54 27.68 -
Num. residues----2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323032
X-RAY DIFFRACTIONf_angle_d0.59431384
X-RAY DIFFRACTIONf_chiral_restr0.043252
X-RAY DIFFRACTIONf_plane_restr0.0044104
X-RAY DIFFRACTIONf_dihedral_angle_d15.93513388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.15250.28381450.22881261399
2.1525-2.21060.30351420.22741262099
2.2106-2.27560.24751430.22271262299
2.2756-2.34890.2731400.21271240797
2.3489-2.43270.25361480.202112706100
2.4327-2.52990.23141400.19771263199
2.5299-2.64480.26641420.19731266499
2.6448-2.78390.25131440.19951267599
2.7839-2.95780.22671420.19591269999
2.9578-3.18540.26961440.19371247698
3.1854-3.50440.20141380.17491265199
3.5044-4.00790.21011440.15411271499
4.0079-5.03610.17681460.14251258198
5.0361-19.9920.18581490.15641279699

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