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- PDB-8czp: 2.25 angstrom resolution crystal structure of as-isolated KatG fr... -

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Basic information

Entry
Database: PDB / ID: 8czp
Title2.25 angstrom resolution crystal structure of as-isolated KatG from Mycobacterium tuberculosis with an MYW cofactor
ComponentsCatalase-peroxidase
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 / Catalase-peroxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLi, J. / Liu, A.
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
DepositionMay 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)162,8546
Polymers161,5032
Non-polymers1,3514
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-103 kcal/mol
Surface area50460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.699, 150.699, 155.491
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 80751.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: katG, ERS007661_00994, ERS024276_01596 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5ZBI4, catalase-peroxidase
#2: 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
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 6% PEG4000, 0.1M NA 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: 0.97946 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 21, 2022
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 83641 / % possible obs: 98.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 30.15 Å2 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.099 / Rrim(I) all: 0.223 / Χ2: 1.042 / Net I/σ(I): 3.6 / Num. measured all: 410612
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.294.60.98241710.320.5021.1091.0999.3
2.29-2.334.50.82741520.6760.4270.9360.8599.4
2.33-2.385.10.80341980.6980.3920.8980.84699.6
2.38-2.4250.73641770.6920.3620.8240.84799.5
2.42-2.4850.64941840.7390.3190.7270.86699.7
2.48-2.5350.57441990.7940.2820.6430.8899.5
2.53-2.64.90.52341800.8360.2590.5860.8899.3
2.6-2.674.90.54341600.830.2640.6071.03398.9
2.67-2.754.80.44741820.6990.2250.5031.11998.7
2.75-2.834.40.36441630.8740.1910.4140.98798.4
2.83-2.945.10.32841700.8870.1620.3670.9598.8
2.94-3.055.10.27841780.8880.1390.3121.03698.5
3.05-3.195.10.23341660.9250.1160.2621.05898.4
3.19-3.3650.19841850.9240.10.2231.23198.3
3.36-3.574.90.18541530.9310.0940.2091.57997.4
3.57-3.854.70.15141740.9480.0780.1711.49597.2
3.85-4.235.20.12641600.9720.0620.1411.30397.2
4.23-4.855.10.10242040.980.050.1140.96696.8
4.85-6.14.80.09141750.9840.0460.1020.76795.4
6.1-504.90.10343100.9810.0510.1161.06593.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SJ2

1sj2


Resolution: 2.25→37.675 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2834 2010 2.4 %
Rwork0.2401 81570 -
obs0.2412 83580 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.19 Å2 / Biso mean: 26.5238 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 2.25→37.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11058 0 94 608 11760
Biso mean--22.29 26.48 -
Num. residues----1434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111470
X-RAY DIFFRACTIONf_angle_d1.04615641
X-RAY DIFFRACTIONf_chiral_restr0.0591626
X-RAY DIFFRACTIONf_plane_restr0.0062052
X-RAY DIFFRACTIONf_dihedral_angle_d15.9286668
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.30570.38771470.3563577899
2.3057-2.36810.39541310.3412581999
2.3681-2.43770.36781540.33165846100
2.4377-2.51640.40241430.32715839100
2.5164-2.60630.36781420.3183583499
2.6063-2.71060.38781350.3198580999
2.7106-2.8340.37391460.3011582099
2.834-2.98330.34771470.2871580499
2.9833-3.17010.30631390.2737582698
3.1701-3.41480.30111460.2427580798
3.4148-3.75810.23751440.2165579397
3.7581-4.30130.21091390.1874583097
4.3013-5.41660.22091430.1702581396
5.4166-37.6750.20251540.1632595294

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