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- PDB-8w1y: 2.30 angstrom resolution intermediate crystal structure of KatG f... -

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Basic information

Entry
Database: PDB / ID: 8w1y
Title2.30 angstrom resolution intermediate crystal structure of KatG from Mycobacterium tuberculosis with an MYW-OOH cofactor soaked with peroxide for 1 minute
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
PROTOPORPHYRIN IX CONTAINING FE / Catalase-peroxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, J. / Duan, R. / 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
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

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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)326,06116
Polymers323,1344
Non-polymers2,92612
Water23,2211289
1
A: Catalase-peroxidase
B: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0308
Polymers161,5672
Non-polymers1,4636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Catalase-peroxidase
D: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0308
Polymers161,5672
Non-polymers1,4636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.511, 150.511, 155.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

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


Mass: 80783.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: katG, ERS007661_00994, ERS053720_01149 / 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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1289 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.3 %
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: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 152326 / % possible obs: 98 % / Redundancy: 2.5 % / CC1/2: 0.965 / CC star: 0.991 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.13 / Rrim(I) all: 0.214 / Χ2: 1.018 / Net I/σ(I): 3.8 / Num. measured all: 375359
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.29-2.332.40.97877100.3630.730.7721.2510.73499.8
2.33-2.372.40.89177310.3880.7480.7041.1410.76399.7
2.37-2.422.40.79477080.4140.7650.6261.0160.77299.7
2.42-2.472.40.71577390.4980.8160.5640.9150.77299.6
2.47-2.522.40.59376760.5660.850.4660.7580.77799.5
2.52-2.582.40.55277360.6220.8760.4330.7050.80299.5
2.58-2.642.40.48376760.6890.9030.3780.6160.899.2
2.64-2.722.50.43576790.7250.9170.3390.5540.80199.2
2.72-2.792.40.3876910.7670.9320.2970.4850.82999.1
2.79-2.892.50.33776830.7930.940.2620.4290.8598.8
2.89-2.992.50.27676290.8590.9610.2140.3510.87598.5
2.99-3.112.50.23176260.9110.9760.1770.2920.92198.3
3.11-3.252.50.18476250.9370.9840.1410.2330.95598.1
3.25-3.422.50.14876170.9570.9890.1130.1881.01197.8
3.42-3.632.50.12275260.9650.9910.0920.1541.10897.2
3.63-3.922.50.10775710.9610.990.080.1351.34197.1
3.92-4.312.50.08175250.9840.9960.0610.1021.09396.6
4.31-4.932.50.0774750.9870.9970.0530.0881.00495.9
4.93-6.212.60.07273970.9890.9970.0530.090.98994.6
6.21-502.60.05673060.9890.9970.0410.073.08592.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SJ2

1sj2


Resolution: 2.3→48.93 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 1961 1.33 %
Rwork0.1913 --
obs0.192 147771 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22300 0 24 1289 23613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922952
X-RAY DIFFRACTIONf_angle_d1.0831292
X-RAY DIFFRACTIONf_dihedral_angle_d8.3893136
X-RAY DIFFRACTIONf_chiral_restr0.0523252
X-RAY DIFFRACTIONf_plane_restr0.014100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.33091330.295810433X-RAY DIFFRACTION96
2.35-2.420.36441520.282210512X-RAY DIFFRACTION98
2.42-2.490.32731450.269610518X-RAY DIFFRACTION97
2.49-2.570.35031500.261210483X-RAY DIFFRACTION97
2.57-2.660.31691440.25810564X-RAY DIFFRACTION97
2.66-2.770.31781340.248610522X-RAY DIFFRACTION97
2.77-2.890.31771380.238110504X-RAY DIFFRACTION97
2.89-3.050.31131430.223710425X-RAY DIFFRACTION97
3.05-3.240.26061340.208510443X-RAY DIFFRACTION97
3.24-3.490.24831460.192310501X-RAY DIFFRACTION97
3.49-3.840.23721410.166210371X-RAY DIFFRACTION96
3.84-4.390.19521400.141610345X-RAY DIFFRACTION95
4.39-5.530.18221330.131410217X-RAY DIFFRACTION94
5.53-48.930.1371280.13199972X-RAY DIFFRACTION91

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