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- PDB-8ff7: Cytosolic ascorbate peroxidase mutant from Panicum virgatum- asco... -

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Basic information

Entry
Database: PDB / ID: 8ff7
TitleCytosolic ascorbate peroxidase mutant from Panicum virgatum- ascorbate complex
ComponentsCytosolic ascorbate peroxidase
KeywordsOXIDOREDUCTASE / ascorbate peroxidase / ascorbate / heme / hydrogen peroxide / switchgrass
Function / homology
Function and homology information


L-ascorbate peroxidase
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 speciesPanicum virgatum (switchgrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 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: Int J Mol Sci / Year: 2023
Title: Activity of Cytosolic Ascorbate Peroxidase (APX) from Panicum virgatum against Ascorbate and Phenylpropanoids.
Authors: Zhang, B. / Lewis, J.A. / Kovacs, F. / Sattler, S.E. / Sarath, G. / Kang, C.
History
DepositionDec 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Cytosolic ascorbate peroxidase
B: Cytosolic ascorbate peroxidase
C: Cytosolic ascorbate peroxidase
D: Cytosolic ascorbate peroxidase
E: Cytosolic ascorbate peroxidase
F: Cytosolic ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,70424
Polymers163,8116
Non-polymers4,89418
Water16,376909
1
A: Cytosolic ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1174
Polymers27,3021
Non-polymers8163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytosolic ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1174
Polymers27,3021
Non-polymers8163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytosolic ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1174
Polymers27,3021
Non-polymers8163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytosolic ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1174
Polymers27,3021
Non-polymers8163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytosolic ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1174
Polymers27,3021
Non-polymers8163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytosolic ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1174
Polymers27,3021
Non-polymers8163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.267, 80.176, 80.166
Angle α, β, γ (deg.)104.55, 101.97, 110.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytosolic ascorbate peroxidase


Mass: 27301.795 Da / Num. of mol.: 6 / Mutation: C4S, E14D, C168A, V221A, K229D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Panicum virgatum (switchgrass) / Gene: PVAP13_9KG480900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T0NWI5
#2: Sugar
ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H8O6 / Comment: medication*YM
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 909 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging 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: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.194→49.23 Å / Num. obs: 83162 / % possible obs: 97.17 % / Redundancy: 2.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.1267 / Net I/σ(I): 6.45
Reflection shellResolution: 2.194→2.273 Å / Redundancy: 7 % / Rmerge(I) obs: 1.54 / Num. unique obs: 7756 / Χ2: -7 / % possible all: 4.5

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DJR

8djr


Resolution: 2.194→49.23 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 1993 2.4 %
Rwork0.188 --
obs0.1893 82914 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11868 0 6 909 12783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812198
X-RAY DIFFRACTIONf_angle_d1.00916602
X-RAY DIFFRACTIONf_dihedral_angle_d17.2454536
X-RAY DIFFRACTIONf_chiral_restr0.0441698
X-RAY DIFFRACTIONf_plane_restr0.0082184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.194-2.250.3271300.26055289X-RAY DIFFRACTION89
2.25-2.310.29981360.23685685X-RAY DIFFRACTION96
2.31-2.380.30331440.23295746X-RAY DIFFRACTION97
2.38-2.450.27791450.21985794X-RAY DIFFRACTION97
2.45-2.540.32271430.21595789X-RAY DIFFRACTION98
2.54-2.640.24171430.21475830X-RAY DIFFRACTION98
2.64-2.760.28431440.21725842X-RAY DIFFRACTION98
2.76-2.910.32981510.21615805X-RAY DIFFRACTION98
2.91-3.090.30931350.22375802X-RAY DIFFRACTION98
3.09-3.330.26621400.20745865X-RAY DIFFRACTION98
3.33-3.670.23711470.18745818X-RAY DIFFRACTION99
3.67-4.20.2131500.15495884X-RAY DIFFRACTION99
4.2-5.290.18831400.14295873X-RAY DIFFRACTION99
5.29-49.230.15231450.14655899X-RAY DIFFRACTION99

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