[English] 日本語
Yorodumi
- PDB-2km0: Cu(I)-bound CopK -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2km0
TitleCu(I)-bound CopK
ComponentsCopper resistance protein K
KeywordsMETAL BINDING PROTEIN / heavy metal resistance / periplasmic copper binding protein / Copper / Periplasm / Plasmid
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
Copper resistance protein K / Copper resistance protein K / CopK superfamily / Copper resistance protein K / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Copper resistance protein K
Similarity search - Component
Biological speciesRalstonia metallidurans (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsBersch, B.
Citation
Journal: J.Am.Chem.Soc. / Year: 2010
Title: CopK from Cupriavidus metallidurans CH34 Binds Cu(I) in a Tetrathioether Site: Characterization by X-ray Absorption and NMR Spectroscopy
Authors: Sarret, G. / Favier, A. / Hazemann, J.L. / Mergeay, M. / Bersch, B.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge
Authors: Bersch, B. / Favier, A. / Schanda, P. / van Aelst, S. / Vallaeys, T. / Coves, J. / Mergeay, M. / Wattiez, R.
History
DepositionJul 15, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 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_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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: Copper resistance protein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3582
Polymers8,2951
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Copper resistance protein K


Mass: 8294.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia metallidurans (bacteria) / Strain: CH34 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58AD3
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: CopK protein bound to a single Cu(I)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1323D 1H-13C NOESY
1432D 1H-1H NOESY
1523D HNCO
1623D HN(CA)CB
1723D HN(COCA)CB
1823D HNCA
1923D C(CO)NH
11023D (H)CCH-TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] CopK-1, 0.95 mM COPPER(I) ION-2, 50 mM ammonium acetate-3, 10 mM sodium ascorbate-4, 90% H2O/10% D2O90% H2O/10% D2O
21.6 mM [U-100% 13C; U-100% 15N] CopK-5, 1.5 mM COPPER(I) ION-6, 50 mM ammonium acetate-7, 16 mM sodium ascorbate-8, 90% H2O/10% D2O90% H2O/10% D2O
31.5 mM CopK-9, 1.4 mM COPPER(I) ION-10, 50 mM ammonium acetate-11, 14 mM sodium ascorbate-12, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCopK-1[U-100% 15N]1
0.95 mMCOPPER(I) ION-21
50 mMammonium acetate-31
10 mMsodium ascorbate-41
1.6 mMCopK-5[U-100% 13C; U-100% 15N]2
1.5 mMCOPPER(I) ION-62
50 mMammonium acetate-72
16 mMsodium ascorbate-82
1.5 mMCopK-93
1.4 mMCOPPER(I) ION-103
50 mMammonium acetate-113
14 mMsodium ascorbate-123
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian DirectDriveVarianDirect Drive6001
Varian DirectDriveVarianDirect Drive8002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
AtnosCandidTorsten Herrmannpeak picking
AtnosCandidTorsten Herrmannstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20 / Representative conformer: 1

+
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