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- PDB-8w1x: 2.35-angstrom resolution intermediate crystal structure of KatG f... -

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Basic information

Entry
Database: PDB / ID: 8w1x
Title2.35-angstrom resolution intermediate crystal structure of KatG from Mycobacterium tuberculosis with an MYW-OOH cofactor soaked with peroxide for 5 minutes
Components(Catalase-peroxidase) x 2
KeywordsOXIDOREDUCTASE / Met-Tyr-Trp cofactor / heme-dependent enzyme
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / heme binding / metal ion binding / 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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Catalase-peroxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLiu, A. / Li, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Indole N-Linked Hydroperoxyl Adduct of Protein-Derived Cofactor Modulating Catalase-Peroxidase Functions.
Authors: Li, J. / Duan, R. / Traore, E.S. / Nguyen, R.C. / Davis, I. / Griffth, W.P. / Goodwin, D.C. / Jarzecki, A.A. / Liu, A.
History
DepositionFeb 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,12510
Polymers161,5352
Non-polymers1,5908
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.463, 150.463, 155.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-1230-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Catalase-peroxidase


Mass: 80751.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: katG / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5ZBI4
#2: Protein Catalase-peroxidase / CP / Peroxidase/catalase


Mass: 80783.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: W107 modified to 1-hydroperoxy-L-tryptophan / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: katG, ERS007661_00994, ERS053720_01149 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5ZBI4, catalase-peroxidase

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Non-polymers , 6 types, 629 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 6% PEG4000, 0.1M sodium acetate, 0.17mM N-dodecyl-B-D-maltoside, protein concentration of 15 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 30, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 67568 / % possible obs: 90.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.72 Å2 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.119 / Rrim(I) all: 0.235 / Χ2: 1.058 / Net I/σ(I): 3.7 / Num. measured all: 239629
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.393.40.95133930.4050.5941.1280.83192.6
2.39-2.433.50.90634210.460.5581.0690.87193.3
2.43-2.483.50.79434330.5010.4850.9350.88794
2.48-2.533.50.72134570.5780.4410.850.8893.6
2.53-2.593.50.66334300.6180.4020.780.88693.1
2.59-2.653.50.61834300.6570.3750.7270.91793.2
2.65-2.713.50.5634170.4830.340.6590.96893.1
2.71-2.793.50.48534330.7560.2910.5690.91692.6
2.79-2.873.50.43333940.7830.2590.5070.94492.3
2.87-2.963.50.3634230.8390.2150.4220.98392
2.96-3.073.50.30833850.8860.1820.361.00391.7
3.07-3.193.60.24733860.9250.1450.2881.02291.3
3.19-3.333.60.20533840.950.120.2391.02990.9
3.33-3.513.60.17133620.9620.0990.1981.13190.2
3.51-3.733.60.14733450.9710.0850.1711.19689.8
3.73-4.023.60.12633310.9720.0730.1471.33289
4.02-4.423.60.11133300.9760.0650.131.38488
4.42-5.063.60.09432790.9860.0530.1081.29486.7
5.06-6.373.60.09132700.9880.0510.1050.96485
6.37-503.70.05832650.9940.0320.0671.67280.7

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SJ2

1sj2


Resolution: 2.35→47.72 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 2010 2.98 %
Rwork0.1908 --
obs0.1928 67347 90.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11149 0 20 621 11790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911479
X-RAY DIFFRACTIONf_angle_d1.03515647
X-RAY DIFFRACTIONf_dihedral_angle_d15.7354111
X-RAY DIFFRACTIONf_chiral_restr0.0531626
X-RAY DIFFRACTIONf_plane_restr0.0092052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.36841420.29954623X-RAY DIFFRACTION91
2.41-2.470.37671440.27474763X-RAY DIFFRACTION93
2.47-2.550.32471480.25064743X-RAY DIFFRACTION93
2.55-2.630.34771440.25284764X-RAY DIFFRACTION93
2.63-2.720.33521450.25094695X-RAY DIFFRACTION92
2.72-2.830.33851330.25464740X-RAY DIFFRACTION92
2.83-2.960.33481510.23344698X-RAY DIFFRACTION92
2.96-3.110.2941460.22054675X-RAY DIFFRACTION91
3.11-3.310.28311410.2024674X-RAY DIFFRACTION91
3.31-3.570.24671550.18864661X-RAY DIFFRACTION90
3.57-3.920.22091370.15924635X-RAY DIFFRACTION89
3.92-4.490.20021390.13424602X-RAY DIFFRACTION88
4.49-5.660.1791420.13464542X-RAY DIFFRACTION86
5.66-47.720.17161430.13544522X-RAY DIFFRACTION82

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