[English] 日本語
Yorodumi
- PDB-6p42: Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p42
TitleYeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c
Components
  • Cytochrome c iso-1
  • Cytochrome c peroxidase, mitochondrial
KeywordsElectron transport/Oxidoreductase / heme proteins / electron hopping / multi-step tunneling / electron transport-oxidoreductase complex / ELECTRON TRANSPORT
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cardiolipin binding / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / response to reactive oxygen species ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cardiolipin binding / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. ...Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c isoform 1 / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.905 Å
AuthorsYee, E.F. / Crane, B.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Tuning Radical Relay Residues by Proton Management Rescues Protein Electron Hopping.
Authors: Yee, E.F. / Dzikovski, B. / Crane, B.R.
History
DepositionMay 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c peroxidase, mitochondrial
B: Cytochrome c iso-1
C: Cytochrome c peroxidase, mitochondrial
D: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5138
Polymers90,0474
Non-polymers2,4664
Water905
1
A: Cytochrome c peroxidase, mitochondrial
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2564
Polymers45,0232
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cytochrome c peroxidase, mitochondrial
D: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2564
Polymers45,0232
Non-polymers1,2332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.926, 111.918, 88.747
Angle α, β, γ (deg.)90.000, 105.630, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cytochrome c peroxidase, mitochondrial / CCP


Mass: 33527.211 Da / Num. of mol.: 2 / Mutation: W191Y, L232H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CCP1, CCP, CPO, YKR066C / Plasmid: ppSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Protein Cytochrome c iso-1


Mass: 11496.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Plasmid: PBTR-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00044
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate,175 mM NaCl, 5 mM n-octyl-B-D-glucoside, polyethylene glycol 3350 18%-20%, L-proline
PH range: 5.4-6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17844 / % possible obs: 93.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.07 / Rrim(I) all: 0.178 / Χ2: 0.516 / Net I/σ(I): 2.6 / Num. measured all: 107326
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.952.90.6855360.6820.3950.7990.456.4
2.95-33.31.0116560.3270.571.170.38469.3
3-3.063.80.9127430.450.4721.0340.40676.1
3.06-3.124.20.8067910.6710.3990.9040.41185.3
3.12-3.194.70.678750.8530.3220.7470.42592.7
3.19-3.275.30.6949400.7530.320.7680.41995.5
3.27-3.355.50.6079010.8530.2750.6690.43297.9
3.35-3.445.60.4689310.9230.210.5150.44197.5
3.44-3.546.20.3929790.9390.1680.4280.47199.2
3.54-3.656.90.3649210.9490.1470.3930.47799.9
3.65-3.787.10.2849570.9640.1140.3060.50899.6
3.78-3.9470.2429410.9740.0980.2610.51899.3
3.94-4.1170.1999560.9830.080.2150.55799.8
4.11-4.336.80.1569400.9890.0640.1690.56399.6
4.33-4.66.30.149720.9870.060.1530.57698.8
4.6-4.967.20.1289420.9920.0510.1380.55199.9
4.96-5.467.20.1289490.990.0510.1380.51599.9
5.46-6.246.90.1239710.9910.050.1330.51499.9
6.24-7.866.60.0919600.9940.0380.0990.57398.6
7.86-506.80.0679830.9950.0290.0730.74799.5

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CIH

5cih


Resolution: 2.905→46.817 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 32.78
RfactorNum. reflection% reflection
Rfree0.2708 1604 10.02 %
Rwork0.2119 --
obs0.2179 16004 83.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.61 Å2 / Biso mean: 68.1039 Å2 / Biso min: 30.58 Å2
Refinement stepCycle: final / Resolution: 2.905→46.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6351 0 172 5 6528
Biso mean--69.55 51.36 -
Num. residues----794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9048-2.99860.4661850.349469878346
2.9986-3.10570.4198950.3533923101859
3.1057-3.23010.40871260.311122124872
3.2301-3.3770.37411350.29911249138480
3.377-3.5550.40761490.25661390153987
3.555-3.77760.29661600.22581400156092
3.7776-4.06920.25721630.20621478164195
4.0692-4.47840.26481700.18681507167796
4.4784-5.12570.2181710.17511517168897
5.1257-6.45520.25021730.20761540171398
6.4552-46.82280.19851770.16481576175398

+
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