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- PDB-8u3p: 1.79 Angstrom resolution crystal structure of KatG from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 8u3p
Title1.79 Angstrom resolution crystal structure of KatG from Mycobacterium tuberculosis with an MYW cofactor after heat incubation for 60 minutes
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: 1.79 Å
AuthorsLiu, A. / Li, J. / Ran, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108988 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
DepositionSep 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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
Revision 1.2Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _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)327,36633
Polymers323,0064
Non-polymers4,36029
Water61,9903441
1
A: Catalase-peroxidase
D: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,82118
Polymers161,5032
Non-polymers2,31816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15010 Å2
ΔGint-128 kcal/mol
Surface area49230 Å2
MethodPISA
2
B: Catalase-peroxidase
C: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,54515
Polymers161,5032
Non-polymers2,04213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-118 kcal/mol
Surface area49570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.580, 150.580, 311.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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


Mass: 80751.609 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 3470 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: 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
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3441 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15 mg/mL protein, 6% PEG4000, 0.1 M sodium acetate, 0.17 mM N-dodecyl-B-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2023
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: 1.79→50 Å / Num. obs: 318454 / % possible obs: 95.6 % / Redundancy: 6.2 % / CC1/2: 0.964 / CC star: 0.991 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.093 / Rrim(I) all: 0.24 / Χ2: 1.008 / Net I/σ(I): 3.5 / Num. measured all: 1971087
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.79-1.826.50.724157200.7670.9320.3020.7870.38395.5
1.82-1.856.60.658157230.7970.9420.2730.7150.41395.5
1.85-1.896.50.625157680.8120.9470.2690.6840.48795.5
1.89-1.936.50.568156720.8230.950.2380.6180.55395.1
1.93-1.976.40.494157160.8550.960.2070.5370.54595.2
1.97-2.026.20.44156540.8730.9650.1860.480.5994.7
2.02-2.075.80.433156340.3340.7070.1940.4770.74594.5
2.07-2.126.40.411156830.8770.9670.1660.4450.72694.6
2.12-2.186.30.322156410.9260.9810.1330.350.68294.6
2.18-2.266.20.314156510.9290.9810.1310.3410.78694.5
2.26-2.346.10.275156000.9450.9860.1150.2990.78594.1
2.34-2.435.90.253156830.9440.9860.1080.2770.82694.4
2.43-2.545.60.244156420.9370.9840.1070.2681.04894.2
2.54-2.6760.232158260.9410.9850.0980.2530.98995
2.67-2.845.90.214158790.9470.9860.0910.2331.06395.2
2.84-3.065.70.211161590.9460.9860.0930.2321.23496.7
3.06-3.375.40.19162760.9490.9870.0860.2091.52697
3.37-3.8660.179166320.9640.9910.0770.1951.70298.7
3.86-4.866.20.177166660.970.9920.0730.1922.10598
4.86-507.40.168172290.9810.9950.0640.182.55497.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829-000)refinement
SCALEPACKdata scaling
PDB_EXTRACT4.1data extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SJ2

1sj2


Resolution: 1.79→49.554 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 2000 0.63 %
Rwork0.1787 --
obs0.179 318306 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→49.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22116 0 294 3441 25851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723032
X-RAY DIFFRACTIONf_angle_d0.91331372
X-RAY DIFFRACTIONf_dihedral_angle_d3.96614647
X-RAY DIFFRACTIONf_chiral_restr0.0543253
X-RAY DIFFRACTIONf_plane_restr0.0064106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7905-1.83520.33181400.270522159X-RAY DIFFRACTION95
1.8352-1.88490.29531410.244722324X-RAY DIFFRACTION95
1.8849-1.94030.28561410.228422307X-RAY DIFFRACTION95
1.9403-2.0030.25091410.216322281X-RAY DIFFRACTION95
2.003-2.07450.25391410.198622192X-RAY DIFFRACTION95
2.0745-2.15760.21751400.184222205X-RAY DIFFRACTION95
2.1576-2.25580.24221410.18322243X-RAY DIFFRACTION95
2.2558-2.37470.22851400.180222179X-RAY DIFFRACTION94
2.3747-2.52350.21161400.181922240X-RAY DIFFRACTION94
2.5235-2.71830.22221420.180422468X-RAY DIFFRACTION95
2.7183-2.99190.22351440.180322745X-RAY DIFFRACTION96
2.9919-3.42470.20371470.168923135X-RAY DIFFRACTION97
3.4247-4.31440.20521490.146423682X-RAY DIFFRACTION99
4.3144-49.5540.18061530.162424146X-RAY DIFFRACTION98

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