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- PDB-8djt: Cytosolic ascorbate peroxidase from Sorghum bicolor - four ascorb... -

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Basic information

Entry
Database: PDB / ID: 8djt
TitleCytosolic ascorbate peroxidase from Sorghum bicolor - four ascorbates complex
ComponentsL-ascorbate peroxidaseAscorbate 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 / 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
ASCORBIC ACID / PROTOPORPHYRIN IX CONTAINING FE / L-ascorbate peroxidase
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 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)28,6888
Polymers27,2521
Non-polymers1,4367
Water6,287349
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)38.296, 75.097, 82.997
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, 5 molecules A

#1: Protein L-ascorbate peroxidase / 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 / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM

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Non-polymers , 4 types, 352 molecules

#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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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 / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
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 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→50 Å / Num. obs: 83614 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 7.95 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Χ2: 0.991 / Net I/σ(I): 9.1 / Num. measured all: 529415
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.16-1.185.70.49640990.8640.2280.5470.902100
1.18-1.26.40.44841610.9060.1930.4890.962100
1.2-1.226.30.41840870.9140.180.4560.995100
1.22-1.256.30.36941230.9260.160.4030.973100
1.25-1.2860.34241750.9270.1530.3751.003100
1.28-1.316.10.2941000.9490.1280.3180.976100
1.31-1.346.50.25141430.9650.1070.2730.996100
1.34-1.386.50.22241570.9720.0940.2410.993100
1.38-1.426.40.20141410.9750.0860.2190.995100
1.42-1.466.10.17341320.980.0760.1891.007100
1.46-1.516.20.13941630.9880.0610.1520.98100
1.51-1.576.60.12141700.9920.0510.1320.993100
1.57-1.656.60.10141660.9930.0420.1090.994100
1.65-1.736.50.08941720.9940.0380.0971.048100
1.73-1.846.20.07841910.9950.0340.0851.044100
1.84-1.986.50.06942000.9960.0290.0751.028100
1.98-2.186.70.06142130.9970.0250.0661.021100
2.18-2.56.30.05842460.9970.0250.0630.976100
2.5-3.156.50.05342940.9970.0220.0580.949100
3.15-506.20.04844810.9980.0210.0520.97699.6

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAG

1oag


Resolution: 1.16→31.55 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1507 2000 2.4 %
Rwork0.1381 81439 -
obs0.1384 83439 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.67 Å2 / Biso mean: 11.565 Å2 / Biso min: 4.14 Å2
Refinement stepCycle: final / Resolution: 1.16→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 168 349 2437
Biso mean--10.5 22.36 -
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 (%)
1.16-1.190.19941390.17975674581399
1.19-1.220.17841420.175657375879100
1.22-1.260.17281400.165157335873100
1.26-1.30.16891420.15857585900100
1.3-1.340.14421420.143257665908100
1.34-1.40.15981410.137257555896100
1.4-1.460.151420.136957785920100
1.46-1.540.16421430.134358135956100
1.54-1.630.14211420.123458035945100
1.63-1.760.12371430.126658295972100
1.76-1.940.15751440.129458375981100
1.94-2.220.13291430.124558726015100
2.22-2.790.14651460.133659246070100
2.79-31.550.15111510.141361606311100

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