[English] 日本語
Yorodumi
- PDB-2cep: ROLE OF MET-230 IN INTRAMOLECULAR ELECTRON TRANSFER BETWEEN THE O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cep
TitleROLE OF MET-230 IN INTRAMOLECULAR ELECTRON TRANSFER BETWEEN THE OXYFERRYL HEME AND TRP 191 IN CYTOCHROME C PEROXIDASE COMPOUND II
ComponentsCYTOCHROME C PEROXIDASE
KeywordsOXIDOREDUCTASE(H2O2(A))
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsHan, G.W. / Miller, M.A. / Kraut, J.
Citation
Journal: Biochemistry / Year: 1994
Title: Role of methionine 230 in intramolecular electron transfer between the oxyferryl heme and tryptophan 191 in cytochrome c peroxidase compound II.
Authors: Liu, R.Q. / Miller, M.A. / Han, G.W. / Hahm, S. / Geren, L. / Hibdon, S. / Kraut, J. / Durham, B. / Millett, F.
#1: Journal: Biochemistry / Year: 1990
Title: X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme Cleft Mutants Prepared by Site-Directed Mutagenesis
Authors: Wang, J. / Mauro, J.M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.-H. / Kraut, J.
#2: Journal: J.Biol.Chem. / Year: 1984
Title: Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7-Angstroms Resolution
Authors: Finzel, B.C. / Poulos, T.L. / Kraut, J.
#3: Journal: Biochemistry / Year: 1987
Title: Yeast Cytochrome C Peroxidase: Mutagenesis and Expression in Escherichia Coli Show Tryptophan-51 is not the Radical Site in Compound I
Authors: Fishel, L.A. / Villafranca, J.E. / Mauro, J.M. / Kraut, J.
History
DepositionMay 31, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3682
Polymers33,7521
Non-polymers6161
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.000, 74.200, 45.400
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


Mass: 33751.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00431, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DIFFERS FROM THAT REPORTED FOR 2CYP AT RESIDUE 272. IN THE PRESENT ENTRY, THIS RESIDUE ...THE SEQUENCE DIFFERS FROM THAT REPORTED FOR 2CYP AT RESIDUE 272. IN THE PRESENT ENTRY, THIS RESIDUE IS REPORTED AS ASN. THIS CORRECTS AN ERROR INTRODUCED IN 2CYP, WHERE THE RESIDUE IS INCORRECTLY REPORTED TO BE ASP. RESIDUES ARE NUMBERED TO BE CONSISTENT WITH THE SEQUENCE OF THE NATIVE (2CYP) STRUCTURE. THUS THE FIRST TWO RESIDUES HAVE RESIDUE NUMBERS -1 AND 0, RESPECTIVELY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, sitting drop / Details: Wang, J., (1990) Biochemistry, 29, 7160.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
250 mMpotassium phosphate1drop
320 %(v/v)MPD1drop
430 %(v/v)MPD1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 18426 / % possible obs: 99 % / Rmerge(I) obs: 0.055

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→20 Å / σ(F): 0
Details: COORDINATES FOR RESIDUES -1, 0 AND 1 ARE NOT INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD NOT BE RESOLVED IN THE FINAL ELECTRON DENSITY MAPS. ALTHOUGH COORDINATES FOR RESIDUE 2 ARE ...Details: COORDINATES FOR RESIDUES -1, 0 AND 1 ARE NOT INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD NOT BE RESOLVED IN THE FINAL ELECTRON DENSITY MAPS. ALTHOUGH COORDINATES FOR RESIDUE 2 ARE INCLUDED, THEY ARE NOT WELL DEFINED DUE TO VERY LARGE TEMPERATURE FACTORS (ABOUT 100 ANGSTROMS SQUARED).
RfactorNum. reflection
obs0.167 18426
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 43 225 2607
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.019
X-RAY DIFFRACTIONp_angle_d0.0470.047
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0680.068
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.82.8
X-RAY DIFFRACTIONp_mcangle_it44
X-RAY DIFFRACTIONp_scbond_it3.43.4
X-RAY DIFFRACTIONp_scangle_it5.15.1
X-RAY DIFFRACTIONp_plane_restr0.0210.021
X-RAY DIFFRACTIONp_chiral_restr0.2040.204
X-RAY DIFFRACTIONp_singtor_nbd0.210.21
X-RAY DIFFRACTIONp_multtor_nbd0.240.24
X-RAY DIFFRACTIONp_xhyhbond_nbd0.240.24
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.53.5
X-RAY DIFFRACTIONp_staggered_tor18.718.7
X-RAY DIFFRACTIONp_orthonormal_tor35.335.3
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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