[English] 日本語
Yorodumi
- PDB-2fee: Structure of the Cl-/H+ exchanger CLC-ec1 from E.Coli in NaBr -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fee
TitleStructure of the Cl-/H+ exchanger CLC-ec1 from E.Coli in NaBr
Components
  • Fab fragment, heavy chain
  • Fab fragment, light chain
  • H(+)/Cl(-) exchange transporter clcA
KeywordsPROTON TRANSPORT / MEMBRANE PROTEIN / CLC-ec1 / CLCA_ECOLI / Chloride/Proton exchange transporter
Function / homology
Function and homology information


chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / chloride transmembrane transport / proton transmembrane transport / identical protein binding / 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
H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAccardi, A. / Walden, M.P. / Nguitragool, W. / Jayaram, H. / Williams, C. / Miller, C.
Citation
Journal: J.Gen.Physiol. / Year: 2005
Title: Separate ion pathways in a Cl-/H+ exchanger
Authors: Accardi, A. / Walden, M.P. / Nguitragool, W. / Jayaram, H. / Williams, C. / Miller, C.
#1: Journal: Science / Year: 2003
Title: Gating the selectivity filter in ClC chloride channels
Authors: Dutzler, R. / Cambell, E.B. / Mackinnon, R.
History
DepositionDec 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H(+)/Cl(-) exchange transporter clcA
B: H(+)/Cl(-) exchange transporter clcA
J: Fab fragment, heavy chain
O: Fab fragment, light chain
I: Fab fragment, heavy chain
L: Fab fragment, light chain


Theoretical massNumber of molelcules
Total (without water)193,1406
Polymers193,1406
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)230.822, 97.684, 170.202
Angle α, β, γ (deg.)90.00, 131.11, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 2 / Auth seq-ID: 18 - 458 / Label seq-ID: 18 - 458

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein H(+)/Cl(-) exchange transporter clcA / ClC-ec1


Mass: 49658.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clcA, eriC / Plasmid: pASK-IBA2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37019
#2: Antibody Fab fragment, heavy chain


Mass: 23823.031 Da / Num. of mol.: 2 / Fragment: Heavy Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 10EC3/G4 / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody Fab fragment, light chain


Mass: 23088.443 Da / Num. of mol.: 2 / Fragment: Light Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 10EC3/G4 / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM NaBr, PEG 400 37% , 0.05 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9198 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 3.2→128.04 Å / Num. obs: 43955 / % possible obs: 99 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 19.1
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.523 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.2refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OTS

1ots


Resolution: 3.2→128.04 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.902 / SU B: 29.189 / SU ML: 0.475 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 1.45 / ESU R Free: 0.526 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29257 2341 5.1 %RANDOM
Rwork0.25144 ---
all0.254 ---
obs0.25357 43955 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 119.602 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å20 Å22.42 Å2
2--3.37 Å20 Å2
3---2.74 Å2
Refinement stepCycle: LAST / Resolution: 3.2→128.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13223 0 0 0 13223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02213553
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.96218456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39651743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09722.985479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.412152145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4491567
X-RAY DIFFRACTIONr_chiral_restr0.0930.22121
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210087
X-RAY DIFFRACTIONr_nbd_refined0.2490.27347
X-RAY DIFFRACTIONr_nbtor_refined0.3190.29330
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2528
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0290.22
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1764tight positional0.040.05
1540medium positional0.360.5
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 182 -
Rwork0.366 3219 -
obs--97.31 %

+
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