[English] 日本語
Yorodumi
- PDB-2qif: Crystal structure of a metallochaperone with a tetranuclear Cu(I)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qif
TitleCrystal structure of a metallochaperone with a tetranuclear Cu(I) cluster
ComponentsCopper chaperone copZ
KeywordsCHAPERONE / TETRANUCLEAR CU(I) CLUSTER
Function / homology
Function and homology information


copper ion transport / copper ion binding / cytoplasm
Similarity search - Function
: / Copper ion binding protein / Heavy metal-associated domain, copper ion-binding / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 ...: / Copper ion binding protein / Heavy metal-associated domain, copper ion-binding / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / COPPER (I) ION / Copper chaperone CopZ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsWest, C. / Singleton, C. / Kihlken, M.A. / Le Brun, N.E. / Hemmings, A.M.
Citation
Journal: Biochemistry / Year: 2009
Title: A tetranuclear Cu(I) cluster in the metallochaperone protein CopZ.
Authors: Hearnshaw, S. / West, C. / Singleton, C. / Zhou, L. / Kihlken, M.A. / Strange, R.W. / Le Brun, N.E. / Hemmings, A.M.
#1: Journal: Biochem.J. / Year: 2002
Title: Copper-mediated dimerization of CopZ, a predicted copper chaperone from Bacillus subtilis
Authors: Kihlken, M.A. / Leech, A.P. / Le Brun, N.E.
History
DepositionJul 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 chaperone copZ
B: Copper chaperone copZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,19710
Polymers14,6922
Non-polymers5048
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-65 kcal/mol
Surface area7650 Å2
MethodPISA
2
A: Copper chaperone copZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6836
Polymers7,3461
Non-polymers3375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Copper chaperone copZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5134
Polymers7,3461
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)23.440, 74.692, 41.212
Angle α, β, γ (deg.)90.00, 101.55, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS A SINGLE COPY OF THE BIOLOGICAL UNIT

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Copper chaperone copZ / Copper-ion-binding protein


Mass: 7346.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 1A1 / Gene: copZ, yvgY / Plasmid: pMKNC6 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O32221

-
Non-polymers , 5 types, 174 molecules

#2: Chemical
ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 166 / 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: 1.98 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 277 K / Method: vapor batch / pH: 4.6
Details: Crystallization by vapour batch using 12 microL drops in Terasaki plates covered with a thin layer of silicone oil and equilibrated against 10 % (v/v) isopropanol (24 h) then 20% (v/v) ...Details: Crystallization by vapour batch using 12 microL drops in Terasaki plates covered with a thin layer of silicone oil and equilibrated against 10 % (v/v) isopropanol (24 h) then 20% (v/v) isopropanol for 4 days. 15% (v/v) glycerol added as cryoprotectant., pH 4.6, VAPOUR BATCH, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2002
Details: mirror; vertical focusing, glancing angle 3.5 mrad, 7.0 Ang. cut off, 1.2m long silicon substrate, rhodium coated, distance from source 16m
RadiationMonochromator: Si 111 optimised for 0.979 or 1.2 wavelength, horizontally focusing, distance from source 18m
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 41550 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Χ2: 2.19 / Net I/σ(I): 25.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 12.4 / Num. unique all: 3783 / Rsym value: 0.45 / Χ2: 2.636 / % possible all: 84.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
SHELXphasing
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.5→10 Å / Num. parameters: 11523 / Num. restraintsaints: 14831
Isotropic thermal model: INDIVIDUAL ATOMIC ANISOTROPIC TEMPERATURE FACTOR REFINEMENT
Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 1073 -RANDOM
all0.1302 20281 --
obs0.1302 20281 95.9 %-
Refine analyzeNum. disordered residues: 14 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1191.22
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1007 0 19 166 1192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0258
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.072

+
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