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- PDB-8djs: Cytosolic ascorbate peroxidase from Sorghum bicolor - one ascorba... -

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Basic information

Entry
Database: PDB / ID: 8djs
TitleCytosolic ascorbate peroxidase from Sorghum bicolor - one ascorbate 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
ASCORBIC ACID / PROTOPORPHYRIN IX CONTAINING FE / L-ascorbate peroxidase
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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)28,1595
Polymers27,2521
Non-polymers9084
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)38.152, 74.730, 82.954
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 / Sugars , 2 types, 2 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
#3: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM

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Non-polymers , 4 types, 331 molecules

#2: 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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: 2.17 Å3/Da / Density % sol: 43.31 %
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: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.19→41.48 Å / Num. obs: 72524 / % possible obs: 94.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 9.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.033 / Rrim(I) all: 0.082 / Net I/σ(I): 13 / Num. measured all: 418318
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
1.19-1.211.20.521162713870.6140.5210.737138.1
6.52-41.4860.04233465570.9980.0180.04638.199.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAG

1oag


Resolution: 1.19→41.48 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1556 2000 2.76 %
Rwork0.1467 70448 -
obs0.1469 72448 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.81 Å2 / Biso mean: 13.6237 Å2 / Biso min: 5.86 Å2
Refinement stepCycle: final / Resolution: 1.19→41.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 108 328 2356
Biso mean--11.45 24.92 -
Num. residues----250
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.19-1.220.3049690.28832462253147
1.22-1.250.25531290.23124495462485
1.25-1.290.22441390.20734929506893
1.29-1.330.16511450.1815085523096
1.33-1.380.21251460.16615161530798
1.38-1.430.15781490.15652485397100
1.43-1.50.15441510.145253135464100
1.5-1.580.15021510.144153065457100
1.58-1.680.15351510.137553065457100
1.68-1.810.13521510.134253465497100
1.81-1.990.15581520.129253495501100
1.99-2.280.13511530.125253725525100
2.28-2.870.11961540.132754315585100
2.87-41.480.16231600.147256455805100

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