[English] 日本語
Yorodumi
- PDB-6z8s: Copper transporter OprC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z8s
TitleCopper transporter OprC
ComponentsPutative copper transport outer membrane porin OprC
KeywordsMEMBRANE PROTEIN / copper transporter / TBDT / Pseudomonas aeruginosa / OprC
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / cell outer membrane
Similarity search - Function
TonB-dependent copper receptor / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain
Similarity search - Domain/homology
COPPER (I) ION / Copper transport outer membrane porin OprC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsBhamidimarri, S.P. / van den Berg, B.
CitationJournal: Plos Biol. / Year: 2021
Title: Acquisition of ionic copper by the bacterial outer membrane protein OprC through a novel binding site.
Authors: Bhamidimarri, S.P. / Young, T.R. / Shanmugam, M. / Soderholm, S. / Basle, A. / Bumann, D. / van den Berg, B.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative copper transport outer membrane porin OprC
B: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,9324
Polymers158,8052
Non-polymers1272
Water1,928107
1
A: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4662
Polymers79,4021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4662
Polymers79,4021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.100, 195.690, 166.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Putative copper transport outer membrane porin OprC


Mass: 79402.312 Da / Num. of mol.: 2 / Mutation: M325H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: oprC, PA3790 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XD89
#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M NaCl 0.15 M NH4SO4 0.1 M MES 18-22% PEG1000 3 mM CuSO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.351326 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.351326 Å / Relative weight: 1
ReflectionResolution: 2.37→97.85 Å / Num. obs: 103185 / % possible obs: 100 % / Redundancy: 13.27 % / Biso Wilson estimate: 63.4 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 12.46
Reflection shellResolution: 2.37→2.41 Å / Num. unique obs: 10239 / CC1/2: 0.315

-
Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FOK

6fok


Resolution: 2.37→61.02 Å / SU ML: 0.3745 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2517 10012 5.01 %
Rwork0.2187 189710 -
obs0.2203 103039 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.89 Å2
Refinement stepCycle: LAST / Resolution: 2.37→61.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10164 0 2 107 10273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008210418
X-RAY DIFFRACTIONf_angle_d0.987914126
X-RAY DIFFRACTIONf_chiral_restr0.05461458
X-RAY DIFFRACTIONf_plane_restr0.00611886
X-RAY DIFFRACTIONf_dihedral_angle_d14.78651446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.40.36553500.37036237X-RAY DIFFRACTION98.71
2.4-2.430.36773420.36626207X-RAY DIFFRACTION98.14
2.43-2.450.3713190.36056271X-RAY DIFFRACTION98.37
2.45-2.490.31933290.35176288X-RAY DIFFRACTION99.34
2.49-2.520.3633340.33966311X-RAY DIFFRACTION99.91
2.52-2.550.36973670.33726317X-RAY DIFFRACTION99.99
2.55-2.590.36113580.34946267X-RAY DIFFRACTION99.92
2.59-2.630.33543130.33786338X-RAY DIFFRACTION99.98
2.63-2.670.35762960.29766473X-RAY DIFFRACTION99.99
2.67-2.710.31623580.28436303X-RAY DIFFRACTION100
2.71-2.760.33043320.26866314X-RAY DIFFRACTION99.91
2.76-2.810.27153010.25376363X-RAY DIFFRACTION99.93
2.81-2.860.29963780.25086295X-RAY DIFFRACTION99.93
2.86-2.920.27943620.2516341X-RAY DIFFRACTION99.93
2.92-2.990.29563350.23186337X-RAY DIFFRACTION99.93
2.99-3.060.26323020.23996364X-RAY DIFFRACTION99.99
3.06-3.130.29213410.2446313X-RAY DIFFRACTION99.95
3.13-3.220.28453560.23796333X-RAY DIFFRACTION99.9
3.22-3.310.27513200.22476349X-RAY DIFFRACTION100
3.31-3.420.23993080.2166331X-RAY DIFFRACTION99.7
3.42-3.540.2633530.20766311X-RAY DIFFRACTION99.67
3.54-3.680.23543250.21246332X-RAY DIFFRACTION99.94
3.68-3.850.25533800.21546279X-RAY DIFFRACTION99.97
3.85-4.050.24573120.20856367X-RAY DIFFRACTION99.93
4.05-4.310.23323800.20066278X-RAY DIFFRACTION99.95
4.31-4.640.2173080.17576390X-RAY DIFFRACTION99.96
4.64-5.10.1762680.17516382X-RAY DIFFRACTION99.98
5.11-5.840.23323330.19376350X-RAY DIFFRACTION99.99
5.84-7.360.22293210.19186375X-RAY DIFFRACTION99.97
7.36-61.020.21053310.19876294X-RAY DIFFRACTION99.34
Refinement TLS params.Method: refined / Origin x: 29.313023248 Å / Origin y: 33.9529728111 Å / Origin z: 41.3214060176 Å
111213212223313233
T0.493210329426 Å2-0.0244459024447 Å2-0.0109392375468 Å2-0.48321333629 Å2-0.000353585292553 Å2--0.468169864614 Å2
L0.222660129747 °2-0.0313609605157 °2-0.197476080317 °2-0.502803894432 °20.322701964043 °2--0.590758193584 °2
S0.0496777706664 Å °-0.0442553427521 Å °0.0554770731448 Å °0.0581765916726 Å °-0.035800072258 Å °0.0231953944072 Å °-0.056804366574 Å °0.0443472337646 Å °-0.0162343799701 Å °
Refinement TLS groupSelection details: all

+
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