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- PDB-7opt: Crystal structure of Trypanosoma cruzi peroxidase -

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Basic information

Entry
Database: PDB / ID: 7opt
TitleCrystal structure of Trypanosoma cruzi peroxidase
ComponentsAscorbate peroxidase
KeywordsOXIDOREDUCTASE / heme peroxidase
Function / homology
Function and homology information


L-ascorbate peroxidase / L-ascorbate peroxidase activity / cellular response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Haem peroxidase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Ascorbate peroxidase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsFreeman, S.L. / Kwon, H. / Skafar, V. / Fielding, A.J. / Martinez, A. / Piacenza, L. / Radi, R. / Raven, E.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structure of Trypanosoma cruzi heme peroxidase and characterization of its substrate specificity and compound I intermediate.
Authors: Freeman, S.L. / Skafar, V. / Kwon, H. / Fielding, A.J. / Moody, P.C.E. / Martinez, A. / Issoglio, F.M. / Inchausti, L. / Smircich, P. / Zeida, A. / Piacenza, L. / Radi, R. / Raven, E.L.
History
DepositionJun 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ascorbate peroxidase
B: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,84213
Polymers73,1012
Non-polymers1,74111
Water3,513195
1
A: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4377
Polymers36,5501
Non-polymers8876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4056
Polymers36,5501
Non-polymers8555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.615, 71.615, 253.289
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ascorbate peroxidase / Ascorbate-dependent peroxidase


Mass: 36550.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: APX, C3747_335g5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I1N3, L-ascorbate peroxidase

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Non-polymers , 5 types, 206 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11-K, -H, -L20.5
ReflectionResolution: 2.02→62.02 Å / Num. obs: 50314 / % possible obs: 99.7 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19
Reflection shellResolution: 2.02→2.07 Å / Rmerge(I) obs: 1.4 / Num. unique obs: 3670

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RIV

3riv


Resolution: 2.02→62 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23 --RANDOM
Rwork0.16 ---
obs-42608 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.02→62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 112 195 4575

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