[English] 日本語
Yorodumi
- PDB-6wje: Copper resistance protein copG- Form 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wje
TitleCopper resistance protein copG- Form 2
Components(DUF411 domain-containing ...) x 2
KeywordsMETAL BINDING PROTEIN / metal resistance copper-binding protein
Function / homologyProtein of unknown function DUF411 / Protein of unknown function, DUF / ACETATE ION / COPPER (II) ION / : / Metal-binding protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHausrath, A.C. / Ly, A.T. / McEvoy, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079192 United States
Citation
Journal: J.Biol.Chem. / Year: 2020
Title: The bacterial copper resistance protein CopG contains a cysteine-bridged tetranuclear copper cluster.
Authors: Hausrath, A.C. / Ramirez, N.A. / Ly, A.T. / McEvoy, M.M.
#1: Journal: To Be Published
Title: Copper resistance protein copG- Form 2
Authors: Hausrath, A.C. / Ly, A.T. / McEvoy, M.M.
History
DepositionApr 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 19, 2020Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn_type.id
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DUF411 domain-containing protein
B: DUF411 domain-containing protein
C: DUF411 domain-containing protein
D: DUF411 domain-containing protein
E: DUF411 domain-containing protein
F: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,25164
Polymers80,5146
Non-polymers3,73758
Water2,288127
1
A: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,11612
Polymers13,4081
Non-polymers70811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9269
Polymers13,4081
Non-polymers5188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,20913
Polymers13,4401
Non-polymers76912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,08211
Polymers13,4401
Non-polymers64210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,05711
Polymers13,4081
Non-polymers64910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: DUF411 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8618
Polymers13,4081
Non-polymers4527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.700, 87.460, 143.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name N or name...
21(chain B and ((resid 1 and (name N or name...
31(chain C and ((resid 1 and (name N or name...
41(chain D and ((resid 1 and (name N or name...
51(chain E and (resid 1 through 12 or resid 14...
61(chain F and ((resid 1 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLU(chain A and ((resid 1 and (name N or name...AA11
12GLUGLUHOHHOH(chain A and ((resid 1 and (name N or name...AA - MB1 - 3061
13GLUGLUHOHHOH(chain A and ((resid 1 and (name N or name...AA - MB1 - 3061
14GLUGLUHOHHOH(chain A and ((resid 1 and (name N or name...AA - MB1 - 3061
15GLUGLUHOHHOH(chain A and ((resid 1 and (name N or name...AA - MB1 - 3061
21GLUGLUGLUGLU(chain B and ((resid 1 and (name N or name...BB11
22GLUGLUHOHHOH(chain B and ((resid 1 and (name N or name...BB - NB1 - 3061
23GLUGLUHOHHOH(chain B and ((resid 1 and (name N or name...BB - NB1 - 3061
24GLUGLUHOHHOH(chain B and ((resid 1 and (name N or name...BB - NB1 - 3061
25GLUGLUHOHHOH(chain B and ((resid 1 and (name N or name...BB - NB1 - 3061
31GLUGLUGLUGLU(chain C and ((resid 1 and (name N or name...CC11
32GLUGLUHOHHOH(chain C and ((resid 1 and (name N or name...CC - OB1 - 3061
33GLUGLUHOHHOH(chain C and ((resid 1 and (name N or name...CC - OB1 - 3061
34GLUGLUHOHHOH(chain C and ((resid 1 and (name N or name...CC - OB1 - 3061
35GLUGLUHOHHOH(chain C and ((resid 1 and (name N or name...CC - OB1 - 3061
41GLUGLUGLUGLU(chain D and ((resid 1 and (name N or name...DD11
42GLUGLUHOHHOH(chain D and ((resid 1 and (name N or name...DD - PB1 - 3061
43GLUGLUHOHHOH(chain D and ((resid 1 and (name N or name...DD - PB1 - 3061
44GLUGLUHOHHOH(chain D and ((resid 1 and (name N or name...DD - PB1 - 3061
45GLUGLUHOHHOH(chain D and ((resid 1 and (name N or name...DD - PB1 - 3061
51GLUGLUASNASN(chain E and (resid 1 through 12 or resid 14...EE1 - 121 - 12
52GLYGLYCYSCYS(chain E and (resid 1 through 12 or resid 14...EE14 - 1514 - 15
53LYSLYSLYSLYS(chain E and (resid 1 through 12 or resid 14...EE1717
54GLUGLUHOHHOH(chain E and (resid 1 through 12 or resid 14...EE - QB1 - 3061
55GLUGLUHOHHOH(chain E and (resid 1 through 12 or resid 14...EE - QB1 - 3061
56GLUGLUHOHHOH(chain E and (resid 1 through 12 or resid 14...EE - QB1 - 3061
57GLUGLUHOHHOH(chain E and (resid 1 through 12 or resid 14...EE - QB1 - 3061
61GLUGLUGLUGLU(chain F and ((resid 1 and (name N or name...FF11
62GLUGLUHOHHOH(chain F and ((resid 1 and (name N or name...FF - RB1 - 3061
63GLUGLUHOHHOH(chain F and ((resid 1 and (name N or name...FF - RB1 - 3061
64GLUGLUHOHHOH(chain F and ((resid 1 and (name N or name...FF - RB1 - 3061
65GLUGLUHOHHOH(chain F and ((resid 1 and (name N or name...FF - RB1 - 3061

-
Components

-
DUF411 domain-containing ... , 2 types, 6 molecules ABEFCD

#1: Protein
DUF411 domain-containing protein


Mass: 13408.251 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: FQ758_25220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C0YHL7, UniProt: Q9HV84*PLUS
#2: Protein DUF411 domain-containing protein


Mass: 13440.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: FQ758_25220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C0YHL7, UniProt: Q9HV84*PLUS

-
Non-polymers , 4 types, 185 molecules

#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM Na Cacodylate pH 6.8 200 mM Zn Acetate 19% ethanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→55.42 Å / Num. obs: 28435 / % possible obs: 99.8 % / Redundancy: 6.62 % / CC1/2: 0.996 / Rrim(I) all: 0.148 / Net I/σ(I): 8.93
Reflection shellResolution: 2.5→2.57 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2067 / CC1/2: 0.566

-
Processing

Software
NameVersionClassification
PHENIXdev_3724refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WIS

6wis


Resolution: 2.5→55.42 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 2842 10.02 %
Rwork0.1881 25532 -
obs0.1938 28374 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.91 Å2 / Biso mean: 53.5931 Å2 / Biso min: 24.92 Å2
Refinement stepCycle: final / Resolution: 2.5→55.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 67 127 5644
Biso mean--65.08 53.26 -
Num. residues----754
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2088X-RAY DIFFRACTION3.142TORSIONAL
12B2088X-RAY DIFFRACTION3.142TORSIONAL
13C2088X-RAY DIFFRACTION3.142TORSIONAL
14D2088X-RAY DIFFRACTION3.142TORSIONAL
15E2088X-RAY DIFFRACTION3.142TORSIONAL
16F2088X-RAY DIFFRACTION3.142TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.540.29571390.24371252139199
2.54-2.590.34981400.24212511391100
2.59-2.640.29221400.232512591399100
2.64-2.690.30371390.224612511390100
2.69-2.750.30241410.223212681409100
2.75-2.820.3041390.21412491388100
2.82-2.890.25341410.212661407100
2.89-2.960.26591390.194112491388100
2.96-3.050.31491410.212801421100
3.05-3.150.27831400.199712581398100
3.15-3.260.2761410.19712631404100
3.26-3.390.25781400.202512701410100
3.39-3.550.2211410.182312641405100
3.55-3.730.24911430.17071291143499
3.73-3.970.21141430.171212781421100
3.97-4.270.23971410.160112711412100
4.27-4.70.20121440.1612941438100
4.7-5.380.2291460.182113101456100
5.39-6.780.26031470.20713141461100
6.78-55.420.21491570.186713941551100

+
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://pdbjlvh1.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