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- PDB-5jpr: Neutron Structure of Compound II of Ascorbate Peroxidase -

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Basic information

Entry
Database: PDB / ID: 5jpr
TitleNeutron Structure of Compound II of Ascorbate Peroxidase
ComponentsAscorbate peroxidase
KeywordsOXIDOREDUCTASE / Heme Peroxidase / Intermediate / Ferryle Heme / Compound II / Cryo-trapping
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 / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DEUTERATED WATER / PROTOPORPHYRIN IX CONTAINING FE / : / L-ascorbate peroxidase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.806 Å
AuthorsKwon, H. / Blakeley, M.P. / Raven, E.L. / Moody, P.C.E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K015656/1 United Kingdom
Wellcome TrustWT094104MA United Kingdom
CitationJournal: Nat Commun / Year: 2016
Title: Direct visualization of a Fe(IV)-OH intermediate in a heme enzyme.
Authors: Kwon, H. / Basran, J. / Casadei, C.M. / Fielding, A.J. / Schrader, T.E. / Ostermann, A. / Devos, J.M. / Aller, P. / Blakeley, M.P. / Moody, P.C. / Raven, E.L.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.type_symbol / _pdbx_audit_support.funding_organization
Revision 3.0Oct 3, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Refinement description / Source and taxonomy
Category: atom_site / entity_src_gen / refine
Item: _atom_site.occupancy / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 3.1Nov 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 3.2Mar 6, 2019Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 3.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 3.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ascorbate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2105
Polymers28,3621
Non-polymers8484
Water7,026390
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-45 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.095, 82.095, 75.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-435-

DOD

21A-565-

DOD

31A-697-

DOD

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Components

#1: Protein Ascorbate peroxidase / Cytosolic ascorbate peroxidase 1 / Uncharacterized protein


Mass: 28361.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: apx1, GLYMA_U021900 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.25 M Lithium sulfate, 0.1 M HEPES pH 8.3 - 8.9 / PH range: 8.3 - 8.9

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORILL LADI III13.2 - 4.2
ROTATING ANODERIGAKU MICROMAX-007 HF21.5418
Detector
TypeIDDetectorDateDetails
MAATEL IMAGINE1IMAGE PLATEOct 14, 2015multilayer
RIGAKU SATURN 944+2CCDOct 20, 2015multilayer
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
13.21
24.21
31.54181
Reflection

Entry-ID: 5JPR

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.2-40922069.840.1817
1.8-19.912385798.726.80.1629.4

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Refinement

Baniso 11: 0.4889 Å2 / Baniso 12: -0 Å2 / Baniso 13: -0 Å2 / Baniso 22: 0.4889 Å2 / Baniso 23: 0 Å2 / Baniso 33: -0.9778 Å2 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.4 / Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Starting model: 2XIF

2xif

/ Bsol: 34.834 Å2 / ksol: 0.429 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.806-19.91X-RAY DIFFRACTION0.21590.15470.1578119423857598.7221.36
2.202-36.714NEUTRON DIFFRACTION0.31040.23640.240146292205.0168.1412.03
Refinement stepCycle: LAST / Resolution: 1.806→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 54 390 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164845
X-RAY DIFFRACTIONf_angle_d1.3668082
X-RAY DIFFRACTIONf_dihedral_angle_d11.8981174
X-RAY DIFFRACTIONf_chiral_restr0.115280
X-RAY DIFFRACTIONf_plane_restr0.009850
NEUTRON DIFFRACTIONf_bond_d0.0164845
NEUTRON DIFFRACTIONf_angle_d1.3668082
NEUTRON DIFFRACTIONf_dihedral_angle_d11.8981174
NEUTRON DIFFRACTIONf_chiral_restr0.115280
NEUTRON DIFFRACTIONf_plane_restr0.009850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.806-1.87790.25991240.19132354X-RAY DIFFRACTION94
1.8779-1.96330.23031300.16572470X-RAY DIFFRACTION99
1.9633-2.06670.211330.14712515X-RAY DIFFRACTION100
2.0667-2.1960.21111310.15012500X-RAY DIFFRACTION100
2.196-2.36540.24091310.15362514X-RAY DIFFRACTION99
2.3654-2.60290.241340.15212521X-RAY DIFFRACTION99
2.6029-2.97850.21021310.15652514X-RAY DIFFRACTION99
2.9785-3.74850.19561370.14592575X-RAY DIFFRACTION99
3.7485-19.910.20371430.1562700X-RAY DIFFRACTION99
2.2021-2.52070.39181060.36092024NEUTRON DIFFRACTION48
2.5207-3.17560.3361470.23992768NEUTRON DIFFRACTION65
3.1756-36.710.27352090.19873966NEUTRON DIFFRACTION89

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