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- PDB-8w1w: 2.03 angstrom resolution crystal structure of as-isolated KatG fr... -

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Basic information

Entry
Database: PDB / ID: 8w1w
Title2.03 angstrom resolution crystal structure of as-isolated KatG from Mycobacterium tuberculosis with an MYW-OOH 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: 2.033 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
C: Catalase-peroxidase
D: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,84926
Polymers323,1344
Non-polymers3,71522
Water55,2703068
1
A: Catalase-peroxidase
D: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,33312
Polymers161,5672
Non-polymers1,76510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14700 Å2
ΔGint-138 kcal/mol
Surface area49540 Å2
MethodPISA
2
B: Catalase-peroxidase
C: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,51714
Polymers161,5672
Non-polymers1,95012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15020 Å2
ΔGint-136 kcal/mol
Surface area49500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.674, 150.674, 311.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 3090 molecules

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


Mass: 616.487 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 3068 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
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: Sep 24, 2021
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: 2.03→50 Å / Num. obs: 206789 / % possible obs: 90.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.74 Å2 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.114 / Rrim(I) all: 0.243 / Χ2: 1.015 / Net I/σ(I): 4.1 / Num. measured all: 774943
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.03-2.073.60.983102260.3950.5361.1250.78390.6
2.07-2.13.60.873102340.4080.4750.9990.79490.8
2.1-2.143.60.787102670.70.4260.8990.80390.9
2.14-2.193.60.688102650.740.3720.7860.80790.7
2.19-2.233.60.646102350.7560.3490.7380.81990.9
2.23-2.293.60.556102870.5820.30.6350.90690.8
2.29-2.343.70.49103230.8380.2640.560.85491.2
2.34-2.413.70.434103090.8670.2330.4950.87891
2.41-2.483.70.394103620.890.2110.4490.91491.3
2.48-2.563.70.348103600.8960.1860.3970.94591.2
2.56-2.653.70.318103930.9240.170.3620.93991.5
2.65-2.763.70.283104540.9340.1510.3220.98291.9
2.76-2.883.70.246104340.9460.1310.28191.7
2.88-3.033.70.211105590.9560.1130.2411.07292.4
3.03-3.223.80.183105390.9650.0970.2081.21192.2
3.22-3.473.80.157105480.9660.0840.1791.37392.1
3.47-3.823.90.135105250.9770.0720.1541.4691.3
3.82-4.373.90.113103590.980.060.1291.33689.5
4.37-5.514.10.104101690.9840.0540.1181.14987.1
5.51-504.20.09699410.9830.050.1091.09481.5

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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: 2.033→47.9883 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 1997 0.97 %
Rwork0.1655 204683 -
obs0.1661 206680 90.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.69 Å2 / Biso mean: 17.4894 Å2 / Biso min: 5.35 Å2
Refinement stepCycle: final / Resolution: 2.033→47.9883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22124 0 252 3068 25444
Biso mean--14.41 24.78 -
Num. residues----2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02223041
X-RAY DIFFRACTIONf_angle_d1.66531401
X-RAY DIFFRACTIONf_chiral_restr0.0973257
X-RAY DIFFRACTIONf_plane_restr0.0114114
X-RAY DIFFRACTIONf_dihedral_angle_d12.37313387
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.033-2.08340.27321380.2161412989
2.0834-2.13980.27961420.21351453091
2.1398-2.20270.29221420.20361454691
2.2027-2.27380.28641420.19471453091
2.2738-2.35510.29041420.18821463691
2.3551-2.44940.23911440.18241464291
2.4494-2.56090.23861430.17661467191
2.5609-2.69590.23961440.17551474792
2.6959-2.86480.23291440.17191479592
2.8648-3.08590.23141470.17021493892
3.0859-3.39640.2251460.16171495992
3.3964-3.88770.19811450.14271491691
3.8877-4.89730.14451420.12461456289
4.8973-47.98830.18921360.14381408283

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