[English] 日本語
Yorodumi
- PDB-3nvj: Crystal structure of the C143A/C166A mutant of Ero1p -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nvj
TitleCrystal structure of the C143A/C166A mutant of Ero1p
ComponentsEndoplasmic oxidoreductin-1
KeywordsOXIDOREDUCTASE / flavoenzyme / FAD / disulfide bonds / ER
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / thiol oxidase activity / protein folding in endoplasmic reticulum / protein-disulfide reductase activity / FAD binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Endoplasmic reticulum oxidoreductin 1 / ERO1-like superfamily / Endoplasmic Reticulum Oxidoreductin 1 (ERO1)
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / 1-ETHYL-PYRROLIDINE-2,5-DIONE / Endoplasmic oxidoreductin-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFass, D. / Vonshak, O.
CitationJournal: Protein Sci. / Year: 2010
Title: Steps in reductive activation of the disulfide-generating enzyme Ero1p
Authors: Heldman, N. / Vonshak, O. / Sevier, C.S. / Vitu, E. / Mehlman, T. / Fass, D.
History
DepositionJul 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoplasmic oxidoreductin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3204
Polymers45,2951
Non-polymers1,0253
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.220, 107.220, 124.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

#1: Protein Endoplasmic oxidoreductin-1 / Ero1p / endoplasmic oxidoreductase protein 1


Mass: 45294.898 Da / Num. of mol.: 1 / Fragment: residues in UNP 56-424 / Mutation: C143A,C166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERO1, YML130C, YM4987.05C / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q03103, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Chemical ChemComp-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


Mass: 127.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.64 Å3/Da / Density % sol: 73.51 %

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.514 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 13439 / Num. obs: 13131 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1

-
Processing

Software
NameClassification
StructureStudiodata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RQ1

1rq1


Resolution: 3.2→50 Å / σ(F): 2
RfactorNum. reflection
Rfree0.2998 672
Rwork0.2441 -
obs0.251 13131
all-13439
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 63 12 2920

+
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