[English] 日本語
Yorodumi
- PDB-4cvj: Neutron Structure of Compound I intermediate of Cytochrome c Pero... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cvj
TitleNeutron Structure of Compound I intermediate of Cytochrome c Peroxidase - Deuterium exchanged 100 K
ComponentsCYTOCHROME C PEROXIDASE, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / HEME PEROXIDASE / REDOX / ELECTRON TRANSPORT / FERRIC / HEME / PROTONATION / ENZYME INTERMEDIATE
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / 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 / Cytochrome c peroxidase, mitochondrial / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.182 Å
AuthorsCasadei, C.M. / Gumiero, A. / Blakeley, M.P. / Ostermann, A. / Raven, E.L. / Moody, P.C.E.
CitationJournal: Science / Year: 2014
Title: Neutron Cryo-Crystallography Captures the Protonation State of Ferryl Heme in a Peroxidase
Authors: Casadei, C.M. / Gumiero, A. / Metcalfe, C.L. / Murphy, E.J. / Basran, J. / Concilio, M.G. / Teixeira, S.C.M. / Schrader, T.E. / Fielding, A.J. / Ostermann, A. / Blakeley, M.P. / Raven, E.L. / Moody, P.C.E.
History
DepositionMar 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Jan 25, 2017Group: Data collection
Revision 2.0Jun 28, 2017Group: Atomic model / Data collection / Category: atom_site / diffrn_source
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.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _diffrn_source.type
Revision 2.1Feb 14, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _diffrn_source.type / _pdbx_database_status.status_code_sf
Revision 2.2Nov 14, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME C PEROXIDASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2502
Polymers33,6331
Non-polymers6161
Water5,675315
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.190, 75.830, 107.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CYTOCHROME C PEROXIDASE, MITOCHONDRIAL / CCP / CYTOCHROME C PEROXIDASE


Mass: 33633.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Organ: MITOCHONDRION / Plasmid: PLEICS03 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: D6VXC7, UniProt: P00431*PLUS, cytochrome-c 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-DOD / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: D2O
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): COMPOUND I INTERMEDIATE, OXYGEN BOUND TO FEIV

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growpH: 6 / Details: PH 6.0

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54181.5418
NUCLEAR REACTORFRM II BIODIFF23.393.39
Detector
TypeIDDetectorDateDetails
RIGAKU SATURN 944+1CCDAug 1, 2013OSMIC HF
FRM II 2IMAGE PLATEAug 1, 2013OSMIC HF
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHSINGLE WAVELENGTHneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
23.391
Reflection

Entry-ID: 4CVJ

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(F)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)Observed criterion F maxObserved criterion F minObserved criterion I maxObserved criterion I minScaling rejects
2.18-502205399.34.70.074116.5
2.3-501366190.7002.30.17324.600000
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.18-2.251.70.4285.9194.9
2.5-2.591.70.4281.5271.8

-
Processing

Software
NameVersionClassification
PHENIXphasing
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
Refinement

Baniso 12: 0 Å2 / Baniso 13: 0 Å2 / Baniso 23: 0 Å2 / % reflection Rfree: 5 % / Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBaniso 11 (Å2)Baniso 22 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection obs (%)SU MLDiffraction-IDσ(F)Phase errorBsol (Å2)ksol (e/Å3)
2.182-17.057X-RAY DIFFRACTION0.02132.2575-3.53490.20520.14880.151611042205398.380.211.3817.0323.7560.393
2.501-46.225NEUTRON DIFFRACTION-1.92966.9359-5.00630.2720.18730.19146831366190.670.331.3423.8633.2210.471
Refinement stepCycle: LAST / Resolution: 2.182→17.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 43 315 2714
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0115555
NEUTRON DIFFRACTIONf_angle_d1.2619253
NEUTRON DIFFRACTIONf_dihedral_angle_d15.7571416
NEUTRON DIFFRACTIONf_chiral_restr0.091329
NEUTRON DIFFRACTIONf_plane_restr0.007902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1819-2.2810.20961200.14352286X-RAY DIFFRACTION88
2.281-2.40090.19211370.13992605X-RAY DIFFRACTION100
2.4009-2.55090.21531390.13612623X-RAY DIFFRACTION100
2.5509-2.74710.21181380.14162621X-RAY DIFFRACTION100
2.7471-3.02220.21161390.14882655X-RAY DIFFRACTION100
3.0222-3.45630.21881400.16212658X-RAY DIFFRACTION100
3.4563-4.34270.21071410.1472692X-RAY DIFFRACTION100
4.3427-17.05730.17841500.15842809X-RAY DIFFRACTION100
2.5009-2.69390.29641160.21652208NEUTRON DIFFRACTION78
2.6939-2.9650.31041260.20952401NEUTRON DIFFRACTION86
2.965-3.39390.30011400.192664NEUTRON DIFFRACTION94
3.3939-4.27550.25341470.16542771NEUTRON DIFFRACTION97
4.2755-46.23250.24061540.18312934NEUTRON DIFFRACTION98

+
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://pdbjlvh1.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