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- PDB-7bi1: XFEL crystal structure of soybean ascorbate peroxidase compound II -

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Basic information

Entry
Database: PDB / ID: 7bi1
TitleXFEL crystal structure of soybean ascorbate peroxidase compound II
ComponentsAscorbate peroxidase
KeywordsOXIDOREDUCTASE / Intermediates / Heme protein
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 / 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 / : / L-ascorbate peroxidase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKwon, H. / Tosha, T. / Sugimoto, H. / Raven, E.L. / Moody, P.C.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N015940/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: XFEL Crystal Structures of Peroxidase Compound II.
Authors: Kwon, H. / Basran, J. / Pathak, C. / Hussain, M. / Freeman, S.L. / Fielding, A.J. / Bailey, A.J. / Stefanou, N. / Sparkes, H.A. / Tosha, T. / Yamashita, K. / Hirata, K. / Murakami, H. / ...Authors: Kwon, H. / Basran, J. / Pathak, C. / Hussain, M. / Freeman, S.L. / Fielding, A.J. / Bailey, A.J. / Stefanou, N. / Sparkes, H.A. / Tosha, T. / Yamashita, K. / Hirata, K. / Murakami, H. / Ueno, G. / Ago, H. / Tono, K. / Yamamoto, M. / Sawai, H. / Shiro, Y. / Sugimoto, H. / Raven, E.L. / Moody, P.C.E.
History
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0173
Polymers28,3621
Non-polymers6562
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-21 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.935, 81.935, 75.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

21A-424-

HOH

31A-435-

HOH

41A-632-

HOH

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Components

#1: Protein Ascorbate peroxidase / / Cytosolic ascorbate peroxidase 1 / Uncharacterized protein


Mass: 28361.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: apx1, GLYMA_U021900 / Production host: Escherichia coli (E. coli) / References: UniProt: Q43758, L-ascorbate peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.25 M Lithium sulfate, 0.1 M HEPES pH 8.3 - 8.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.5→58 Å / Num. obs: 41508 / % possible obs: 100 % / Redundancy: 662 % / CC1/2: 0.98 / Net I/σ(I): 11.2
Reflection shellResolution: 1.5→1.51 Å / Num. unique obs: 8746 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
SHELXrefinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JPR

5jpr


Resolution: 1.5→58 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rwork0.14 --
obs-41508 100 %
Displacement parametersBiso max: 114.46 Å2 / Biso mean: 31.6152 Å2 / Biso min: 16.57 Å2
Refinement stepCycle: LAST / Resolution: 1.5→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 44 284 2209

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