[English] 日本語
Yorodumi
- PDB-6tae: Neutron structure of ferric ascorbate peroxidase -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more