[English] 日本語
Yorodumi
- PDB-6q58: Copper loading to a cytosolic copper storage protein from Strepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q58
TitleCopper loading to a cytosolic copper storage protein from Streptomyces lividans (five coppers)
ComponentsCytosolic copper storage protein
KeywordsMETAL BINDING PROTEIN / Copper / cytosolic / storage protein / Streptomyces livdians
Function / homologyProtein of unknown function DUF326 / Copper storage protein / Uncharacterized cysteine-rich protein YhjQ-like / metal ion binding / COPPER (I) ION / Four-helix bundle copper-binding protein
Function and homology information
Biological speciesStreptomyces coelicolor 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsStraw, M.L. / Hough, M.A. / Worrall, J.A.R.
CitationJournal: Chemistry / Year: 2019
Title: A Histidine Residue and a Tetranuclear Cuprous-thiolate Cluster Dominate the Copper Loading Landscape of a Copper Storage Protein from Streptomyces lividans.
Authors: Straw, M.L. / Hough, M.A. / Wilson, M.T. / Worrall, J.A.R.
History
DepositionDec 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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.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_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
B: Cytosolic copper storage protein
C: Cytosolic copper storage protein
D: Cytosolic copper storage protein
A: Cytosolic copper storage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,09519
Polymers50,1414
Non-polymers95315
Water7,620423
1
B: Cytosolic copper storage protein
C: Cytosolic copper storage protein
A: Cytosolic copper storage protein
hetero molecules

D: Cytosolic copper storage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,09519
Polymers50,1414
Non-polymers95315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area8920 Å2
ΔGint-133 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.051, 93.051, 212.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12B
22D
13B
23A
14C
24D
15C
25A
16D
26A

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLYGLYBA19 - 1363 - 120
21VALVALGLYGLYCB19 - 1363 - 120
12ASPASPLEULEUBA20 - 1354 - 119
22ASPASPLEULEUDC20 - 1354 - 119
13VALVALLEULEUBA19 - 1353 - 119
23VALVALLEULEUAD19 - 1353 - 119
14ASPASPLEULEUCB20 - 1354 - 119
24ASPASPLEULEUDC20 - 1354 - 119
15VALVALLEULEUCB19 - 1353 - 119
25VALVALLEULEUAD19 - 1353 - 119
16ASPASPLEULEUDC20 - 1354 - 119
26ASPASPLEULEUAD20 - 1354 - 119

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Cytosolic copper storage protein


Mass: 12535.339 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor 1326 (bacteria)
Gene: SCO3281 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X8F4
#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M Ammonium Sulfate 0.1M MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.33 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 1.5→212.34 Å / Num. obs: 85587 / % possible obs: 98 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Net I/σ(I): 19.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.532.90.65934920.4480.4470.80182.5
8.22-75.348.70.0546280.9940.0180.05896.2

-
Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EI0

6ei0


Resolution: 1.5→212.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.463 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0724 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 4291 5 %RANDOM
Rwork0.1945 ---
obs0.1955 81253 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.19 Å2 / Biso mean: 27.975 Å2 / Biso min: 13.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.5→212.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 15 423 3805
Biso mean--35.42 36.62 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193446
X-RAY DIFFRACTIONr_bond_other_d0.0020.023105
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9464673
X-RAY DIFFRACTIONr_angle_other_deg0.99137182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7175483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.98623.699146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36115566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1631536
X-RAY DIFFRACTIONr_chiral_restr0.0840.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02667
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B69500.13
12C69500.13
21B71560.08
22D71560.08
31B68480.13
32A68480.13
41C68620.13
42D68620.13
51C71600.08
52A71600.08
61D69720.12
62A69720.12
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 269 -
Rwork0.278 4993 -
all-5262 -
obs--82.85 %

+
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