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- PDB-6tae: Neutron structure of ferric ascorbate peroxidase -

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Basic information

Entry
Database: PDB / ID: 6tae
TitleNeutron structure of ferric ascorbate peroxidase
ComponentsAscorbate peroxidase
KeywordsOXIDOREDUCTASE / ascorbate peroxidase / neutron crystallography / heme peroxidase / proton pathway
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
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: 1.9 Å
AuthorsKwon, H. / Basran, J. / Devos, J.M. / Schrader, T.E. / Ostermann, A. / Blakeley, M.P. / Raven, E.L. / Moody, P.C.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N015940/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Visualizing the protons in a metalloenzyme electron proton transfer pathway.
Authors: Kwon, H. / Basran, J. / Devos, J.M. / Suardiaz, R. / van der Kamp, M.W. / Mulholland, A.J. / Schrader, T.E. / Ostermann, A. / Blakeley, M.P. / Moody, P.C.E. / Raven, E.L.
History
DepositionOct 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 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)29,0743
Polymers28,3621
Non-polymers7132
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-32 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.904, 82.904, 75.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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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 (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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestN

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: Lithium Sulfate HEPES

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORILL LADI III12.87-3.4
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDate
MAATEL IMAGINE1IMAGE PLATEOct 1, 2017
RIGAKU SATURN 944+2CCDOct 30, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.871
23.41
31.541
Reflection

Entry-ID: 6TAE / Rmerge(I) obs: 0.1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Diffraction-IDNet I/σ(I)
2.2-36.681013677.53.315.9
1.9-20.112144499.911.2211.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsDiffraction-ID
2.2-2.30.212381
1.9-1.940.714222

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
PDB_EXTRACT3.25data extraction
Refinement

Baniso 11: -3.7555 Å2 / Baniso 12: -0 Å2 / Baniso 13: -0 Å2 / Baniso 22: -3.7555 Å2 / Baniso 23: 0 Å2 / Baniso 33: -5.7725 Å2 / SU ML: 0.19 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 15.82 / Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Starting model: 5JPR

5jpr

/ Bsol: 29.288 Å2 / ksol: 0.399 e/Å3

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)
1.9-20.107X-RAY DIFFRACTION95.0931.176.930.18850.14450.1467107121404599.991.36
2.222-37.076NEUTRON DIFFRACTION0.30760.27630.278508101355.0174.751.79
Refinement stepCycle: final / Resolution: 1.9→20.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 78 368 2351
Biso mean--26.57 38.33 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134230
X-RAY DIFFRACTIONf_angle_d1.5217422
X-RAY DIFFRACTIONf_chiral_restr0.092291
X-RAY DIFFRACTIONf_plane_restr0.007625
X-RAY DIFFRACTIONf_dihedral_angle_d13.9381123
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44550.42491080.40712043NEUTRON DIFFRACTION65
2.4455-2.79920.37061120.37682132NEUTRON DIFFRACTION68
2.7992-3.52630.36371290.29152457NEUTRON DIFFRACTION77
3.5263-37.070.21771590.19182995NEUTRON DIFFRACTION89
1.9-1.98640.25061310.18912487X-RAY DIFFRACTION100
1.9864-2.0910.23681310.16182482X-RAY DIFFRACTION100
2.091-2.22190.20561310.14592509X-RAY DIFFRACTION100
2.2219-2.39320.20411320.13642508X-RAY DIFFRACTION100
2.3932-2.63360.19241330.14482518X-RAY DIFFRACTION100
2.6336-3.01360.20781340.14482527X-RAY DIFFRACTION100
3.0136-3.79260.16831360.14072593X-RAY DIFFRACTION100
3.7926-20.10.15671430.1342709X-RAY DIFFRACTION100

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