[English] 日本語
Yorodumi
- PDB-6k5a: Crystal structure of the E148D/R147A/F317A mutant in presence of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k5a
TitleCrystal structure of the E148D/R147A/F317A mutant in presence of 200 mM NaBr
Components
  • Fab fragment, heavy chainFragment antigen-binding
  • Fab fragment, light chainFragment antigen-binding
  • H(+)/Cl(-) exchange transporter ClcA
KeywordsMEMBRANE PROTEIN / Cl- / H+ antiporter / CLC transporter
Function / homology
Function and homology information


voltage-gated chloride channel activity / antiporter activity / plasma membrane
Similarity search - Function
Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli MS 117-3 (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.162 Å
AuthorsPark, K. / Lim, H.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future Planning19-BR-01-02 Korea, Republic Of
Ministry of Science, ICT and Future Planning2017M3C7A 1048086 Korea, Republic Of
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Mutation of external glutamate residue reveals a new intermediate transport state and anion binding site in a CLC Cl-/H+antiporter.
Authors: Park, K. / Lee, B.C. / Lim, H.H.
History
DepositionMay 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA
C: Fab fragment, heavy chain
D: Fab fragment, light chain
E: Fab fragment, heavy chain
F: Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,57110
Polymers194,2516
Non-polymers3204
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)232.184, 101.338, 172.074
Angle α, β, γ (deg.)90.00, 132.10, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein H(+)/Cl(-) exchange transporter ClcA


Mass: 50214.168 Da / Num. of mol.: 2 / Mutation: R147A, E148D, F317A
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Escherichia coli MS 117-3 (bacteria) / Gene: clcA, eriC, HMPREF9542_03540 / Production host: Escherichia coli (E. coli) / References: UniProt: E9TIA0
#2: Antibody Fab fragment, heavy chain / Fragment antigen-binding


Mass: 23823.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Fab fragment, light chain / Fragment antigen-binding


Mass: 23088.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 400 25% (V/V), 200 mM NaBr 100 mM Glycine

-
Data collection

DiffractionMean temperature: 77.36 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.16→39.7 Å / Num. obs: 98471 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.2
Reflection shellResolution: 3.16→3.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 4868 / CC1/2: 0.795 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ENE

4ene


Resolution: 3.162→39.686 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.36
RfactorNum. reflection% reflection
Rfree0.2757 4921 5 %
Rwork0.2219 --
obs0.2245 98360 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.162→39.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13171 0 4 0 13175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113543
X-RAY DIFFRACTIONf_angle_d1.23718444
X-RAY DIFFRACTIONf_dihedral_angle_d4.2427912
X-RAY DIFFRACTIONf_chiral_restr0.0632123
X-RAY DIFFRACTIONf_plane_restr0.0082314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1617-3.19760.3771160.31182233X-RAY DIFFRACTION71
3.1976-3.23520.29521550.30253138X-RAY DIFFRACTION100
3.2352-3.27470.40571570.30453207X-RAY DIFFRACTION100
3.2747-3.31610.39291960.30633039X-RAY DIFFRACTION100
3.3161-3.35970.40571370.29613264X-RAY DIFFRACTION100
3.3597-3.40570.32461680.28453118X-RAY DIFFRACTION100
3.4057-3.45430.3291630.27683144X-RAY DIFFRACTION100
3.4543-3.50590.32221640.26063203X-RAY DIFFRACTION100
3.5059-3.56060.32291880.26683021X-RAY DIFFRACTION100
3.5606-3.6190.30561880.24953228X-RAY DIFFRACTION100
3.619-3.68130.33061880.25823039X-RAY DIFFRACTION100
3.6813-3.74820.34291970.27253197X-RAY DIFFRACTION100
3.7482-3.82030.35371660.26693119X-RAY DIFFRACTION100
3.8203-3.89820.34871570.26633170X-RAY DIFFRACTION100
3.8982-3.98290.3371320.24853176X-RAY DIFFRACTION100
3.9829-4.07540.28391690.24943159X-RAY DIFFRACTION100
4.0754-4.17720.30211730.23223122X-RAY DIFFRACTION100
4.1772-4.290.26671730.2153122X-RAY DIFFRACTION100
4.29-4.41610.23071800.20023142X-RAY DIFFRACTION100
4.4161-4.55850.27081780.20643146X-RAY DIFFRACTION100
4.5585-4.72110.28211380.20523149X-RAY DIFFRACTION100
4.7211-4.90980.28761730.19993199X-RAY DIFFRACTION100
4.9098-5.13280.2621430.21253121X-RAY DIFFRACTION100
5.1328-5.40280.22861880.19263142X-RAY DIFFRACTION100
5.4028-5.74040.28111360.20333189X-RAY DIFFRACTION100
5.7404-6.18210.24161700.21363123X-RAY DIFFRACTION100
6.1821-6.80140.28571890.20443136X-RAY DIFFRACTION100
6.8014-7.77920.24341620.18483147X-RAY DIFFRACTION100
7.7792-9.77670.18871690.15763157X-RAY DIFFRACTION100
9.7767-39.68950.2661080.23943089X-RAY DIFFRACTION96

+
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