[English] 日本語
Yorodumi
- PDB-1kpl: Crystal Structure of the ClC Chloride Channel from S. typhimurium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kpl
TitleCrystal Structure of the ClC Chloride Channel from S. typhimurium
Componentsputative ClC family, chlorine transport protein
KeywordsMEMBRANE PROTEIN / helical membrane protein / homodimer / ion channel
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PENTADECANE / N-OCTANE / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å
AuthorsDutzler, R. / Campbell, E.B. / Cadene, M. / Chait, B.T. / MacKinnon, R.
CitationJournal: Nature / Year: 2002
Title: X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity.
Authors: Dutzler, R. / Campbell, E.B. / Cadene, M. / Chait, B.T. / MacKinnon, R.
History
DepositionDec 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: putative ClC family, chlorine transport protein
B: putative ClC family, chlorine transport protein
C: putative ClC family, chlorine transport protein
D: putative ClC family, chlorine transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,17816
Polymers201,9984
Non-polymers1,17912
Water362
1
A: putative ClC family, chlorine transport protein
B: putative ClC family, chlorine transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6859
Polymers100,9992
Non-polymers6867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: putative ClC family, chlorine transport protein
D: putative ClC family, chlorine transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4937
Polymers100,9992
Non-polymers4945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.719, 90.159, 80.753
Angle α, β, γ (deg.)90.00, 98.95, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.87657, 0.48126, 0.0038), (0.48002, 0.87481, -0.06545), (-0.03483, -0.05555, -0.99785)62.70105, -15.74265, 5.73088
DetailsThe biologically active assembly is a homodimer. The two biological dimers in the asymmetric unit are composed of protein chains A and B, C and D. Strict crystallograhic NCS constraints have been maintained between the two dimers in the asymmetric unit.

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
putative ClC family, chlorine transport protein / ClC chloride channel


Mass: 50499.586 Da / Num. of mol.: 4 / Mutation: M26L/C264V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pET28b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q8ZRP8

-
Non-polymers , 5 types, 14 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H32
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG 400, acetate, sodium sulfate, lithium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110-15 mg/mlprotein1drop
245 mMn-octyl-beta-maltoside1drop
375 mM1dropNaCl
410 mMTris-HCl1droppH7.5
526-31 %PEG4001reservoir
650 mMsodium acetate1reservoirpH4.6
775-100 mM1reservoirNa2SO4
875-100 mM1reservoirLi2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Oct 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. all: 53397 / Num. obs: 50567 / % possible obs: 94.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 85.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.7
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 1.7 / % possible all: 96.6
Reflection shell
*PLUS
% possible obs: 96.6 %

-
Processing

Software
NameVersionClassification
SHARPphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1592586.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Strict 2-fold NCS constraints between the two dimers in the asymmetric unit were maintained. BULK SOLVENT MODEL USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 4981 10 %RANDOM
Rwork0.254 ---
all0.2583 52912 --
obs0.255 49949 94.4 %-
Displacement parametersBiso mean: 79.6 Å2
Baniso -1Baniso -2Baniso -3
1-26.57 Å20 Å2-11.87 Å2
2--5.33 Å20 Å2
3----31.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13144 0 70 2 13216
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it6.754
X-RAY DIFFRACTIONc_scangle_it9.056
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 808 9.7 %
Rwork0.361 7552 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3ALKANE.PARALKANE.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 79.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_scbond_it6.754
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scangle_it9.056
LS refinement shell
*PLUS
Rfactor Rfree: 0.386 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.361

+
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