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- PDB-7s10: Crystal Structure of ascorbate peroxidase triple mutant: S160M, L... -

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Basic information

Entry
Database: PDB / ID: 7s10
TitleCrystal Structure of ascorbate peroxidase triple mutant: S160M, L203M, Q204M
ComponentsL-ascorbate peroxidase
KeywordsMETAL BINDING PROTEIN / mutant / peroxidase
Function / homology
Function and homology information


L-ascorbate peroxidase / L-ascorbate peroxidase activity / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.40000693677 Å
AuthorsPoulos, T.L. / Kim, J. / Murarka, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131920 United States
CitationJournal: J.Biol.Inorg.Chem. / Year: 2022
Title: Computational analysis of the tryptophan cation radical energetics in peroxidase Compound I.
Authors: Poulos, T.L. / Kim, J.S. / Murarka, V.C.
History
DepositionAug 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: L-ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7985
Polymers26,9511
Non-polymers8484
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.644, 82.644, 75.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

21A-439-

HOH

31A-447-

HOH

41A-660-

HOH

51A-672-

HOH

61A-705-

HOH

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Components

#1: Protein L-ascorbate peroxidase


Mass: 26950.516 Da / Num. of mol.: 1 / Mutation: S160M, L203M, Q204M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: apx1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q43758, L-ascorbate peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: magnesium sulfate / Temp details: room temp

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.4→37 Å / Num. obs: 51578 / % possible obs: 99.38 % / Redundancy: 12.3 % / Biso Wilson estimate: 17.9262833711 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.02982 / Rrim(I) all: 0.1141 / Net I/σ(I): 41.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.4-1.454.10.57421.4848610.8050.27270.642695.16
1.4-1.412.10.0655080.9910.0190.06899.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1oag

1oag


Resolution: 1.40000693677→36.2284873316 Å / SU ML: 0.150449286319 / Cross valid method: THROUGHOUT / σ(F): 1.33772239818 / Phase error: 21.5342511381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.207880099103 1701 3.29881312544 %
Rwork0.171489611336 49863 -
obs0.172654698481 51564 99.3947337985 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.1270949144 Å2
Refinement stepCycle: LAST / Resolution: 1.40000693677→36.2284873316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 54 348 2302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01077513380692076
X-RAY DIFFRACTIONf_angle_d0.8528619894632833
X-RAY DIFFRACTIONf_chiral_restr0.0711946371344289
X-RAY DIFFRACTIONf_plane_restr0.00592183872677368
X-RAY DIFFRACTIONf_dihedral_angle_d6.939137959711201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.40000693677-1.44120.3005688191320.2556710151633867X-RAY DIFFRACTION94.7181430602
1.4412-1.48770.295441298371390.2251116750024076X-RAY DIFFRACTION98.7119437939
1.4877-1.54090.2531246603951400.20233625974100X-RAY DIFFRACTION99.5772663222
1.5409-1.60260.2234295036491410.1914626025184129X-RAY DIFFRACTION99.8830409357
1.6026-1.67550.2374583665171410.1784136257754134X-RAY DIFFRACTION99.8831775701
1.6755-1.76390.2361429349441410.186548800594136X-RAY DIFFRACTION99.9532601075
1.7639-1.87440.2245429952861410.1895053035064135X-RAY DIFFRACTION99.9532491819
1.8744-2.01910.2011191569041430.181784844944182X-RAY DIFFRACTION100
2.0191-2.22220.2025531907291420.1762785051014157X-RAY DIFFRACTION99.976744186
2.2222-2.54370.176006700361430.16913613444229X-RAY DIFFRACTION100
2.5437-3.20450.2287848723561450.1774062532024254X-RAY DIFFRACTION99.9772727273
3.2045-36.22848733160.1874126985211530.1479085636614464X-RAY DIFFRACTION99.9567005845

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