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- PDB-8dju: Cytosolic ascorbate peroxidase from Sorghum bicolor - bicyclic de... -

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Basic information

Entry
Database: PDB / ID: 8dju
TitleCytosolic ascorbate peroxidase from Sorghum bicolor - bicyclic dehydroascorbic acid complex
ComponentsL-ascorbate peroxidase
KeywordsOXIDOREDUCTASE / Cytosolic ascorbate peroxidase
Function / homology
Function and homology information


L-ascorbate peroxidase / L-ascorbate peroxidase activity / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-SIV / L-ascorbate peroxidase
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhang, B. / Kang, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1804699 United States
National Science Foundation (NSF, United States)MCB-2043248 United States
CitationJournal: Plant Physiol. / Year: 2023
Title: A sorghum ascorbate peroxidase with four binding sites has activity against ascorbate and phenylpropanoids.
Authors: Zhang, B. / Lewis, J.A. / Vermerris, W. / Sattler, S.E. / Kang, C.
History
DepositionJul 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: L-ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1795
Polymers27,2521
Non-polymers9284
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.190, 75.303, 83.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein L-ascorbate peroxidase


Mass: 27251.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: SORBI_3001G410200 / Production host: Escherichia coli (E. coli) / References: UniProt: C5WNL8, L-ascorbate peroxidase

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-SIV / (3aS,6S,6aR)-3,3,3a,6-tetrahydroxytetrahydrofuro[3,2-b]furan-2(3H)-one (non-preferred name)


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M Li2SO4, 0.1 M Tris, pH 8.5 and 30 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→38.19 Å / Num. obs: 40092 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Net I/σ(I): 14.2 / Num. measured all: 379116 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.326.24.2721821329440.4151.8714.670.4100
7.12-38.195.70.03925444440.9990.0170.04235.699.4

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAG

1oag


Resolution: 1.5→37.65 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1531 2000 5.09 %
Rwork0.1331 37317 -
obs0.1341 39317 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.14 Å2 / Biso mean: 15.855 Å2 / Biso min: 5.73 Å2
Refinement stepCycle: final / Resolution: 1.5→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 100 328 2348
Biso mean--12.92 29.03 -
Num. residues----250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.540.19481420.182626462788
1.54-1.580.17881400.143126182758
1.58-1.630.17081400.137326152755
1.63-1.680.17511410.143526322773
1.68-1.740.1691420.138126462788
1.74-1.810.14981400.12626112751
1.81-1.890.14561420.120526452787
1.89-1.990.14451420.125226542796
1.99-2.110.15391420.124126502792
2.11-2.280.13821420.120626632805
2.28-2.510.14591440.120226692813
2.51-2.870.14261450.131226922837
2.87-3.610.15961440.13627202864
3.62-37.650.15011540.143428563010

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