[English] 日本語
Yorodumi
- PDB-1ej8: CRYSTAL STRUCTURE OF DOMAIN 2 OF THE YEAST COPPER CHAPERONE FOR S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ej8
TitleCRYSTAL STRUCTURE OF DOMAIN 2 OF THE YEAST COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE (LYS7) AT 1.55 A RESOLUTION
ComponentsLYS7
KeywordsCHAPERONE / beta barrel / copper chaperone for SOD / domain 2
Function / homology
Function and homology information


superoxide dismutase complex / protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / Detoxification of Reactive Oxygen Species / copper ion transport / protein folding chaperone complex / removal of superoxide radicals / mitochondrial intermembrane space / mitochondrial inner membrane / copper ion binding ...superoxide dismutase complex / protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / Detoxification of Reactive Oxygen Species / copper ion transport / protein folding chaperone complex / removal of superoxide radicals / mitochondrial intermembrane space / mitochondrial inner membrane / copper ion binding / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Superoxide dismutase, copper/zinc binding domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase 1 copper chaperone
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.55 Å
AuthorsHall, L.T. / Sanchez, R.J. / Holloway, S.P. / Zhu, H. / Stine, J.E. / Lyons, T.J. / Demeler, B. / Schirf, V. / Hansen, J.C. / Nersissian, A.M. ...Hall, L.T. / Sanchez, R.J. / Holloway, S.P. / Zhu, H. / Stine, J.E. / Lyons, T.J. / Demeler, B. / Schirf, V. / Hansen, J.C. / Nersissian, A.M. / Valentine, J.S. / Hart, P.J.
CitationJournal: Biochemistry / Year: 2000
Title: X-ray crystallographic and analytical ultracentrifugation analyses of truncated and full-length yeast copper chaperones for SOD (LYS7): a dimer-dimer model of LYS7-SOD association and copper delivery.
Authors: Hall, L.T. / Sanchez, R.J. / Holloway, S.P. / Zhu, H. / Stine, J.E. / Lyons, T.J. / Demeler, B. / Schirf, V. / Hansen, J.C. / Nersissian, A.M. / Valentine, J.S. / Hart, P.J.
History
DepositionMar 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry / _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: LYS7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5022
Polymers15,4621
Non-polymers401
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.154, 46.326, 73.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein LYS7


Mass: 15462.370 Da / Num. of mol.: 1 / Fragment: DOMAIN 2
Source method: isolated from a genetically manipulated source
Details: COPPER CHAPERONE FOR YEAST SOD
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P40202
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, CaCl2, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
21 mMEDTA1drop
30.5 mMdithiothreitol1drop
450 mg/mlprotein1drop
5100 mMHEPES1reservoir
628 %PEG4001reservoir
7200 mM1reservoirCaCl2

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→90 Å / Num. all: 17662 / Num. obs: 17203 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.6
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.346 / Num. unique all: 1530 / % possible all: 88.7
Reflection
*PLUS
Num. measured all: 78174
Reflection shell
*PLUS
% possible obs: 88.7 %

-
Processing

Software
NameClassification
SHARPphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.55→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1719 -random
all0.196 17564 --
obs-17195 97.9 %-
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 1 112 1194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d2.2
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 2.2

+
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