[English] 日本語
Yorodumi
- PDB-4kkl: Structure of the E148A mutant of CLC-ec1 delta NC construct in 10... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kkl
TitleStructure of the E148A mutant of CLC-ec1 delta NC construct in 100mM fluoride
Components
  • Fab, heavy chainFragment antigen-binding
  • Fab, light chainFragment antigen-binding
  • H(+)/Cl(-) exchange transporter ClcA
Keywordstranport protein / membrane protein / membrane 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
FLUORIDE ION / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsStockbridge, R.B. / Lim, H.-H. / Miller, C.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Fluoride-dependent interruption of the transport cycle of a CLC Cl(-)/H(+) antiporter.
Authors: Lim, H.H. / Stockbridge, R.B. / Miller, C.
History
DepositionMay 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references

-
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, heavy chain
D: Fab, light chain
E: Fab, heavy chain
F: Fab, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,02010
Polymers188,9446
Non-polymers764
Water0
1
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1976
Polymers95,1212
Non-polymers764
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-44 kcal/mol
Surface area30800 Å2
MethodPISA
2
C: Fab, heavy chain
D: Fab, light chain


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-23 kcal/mol
Surface area19760 Å2
MethodPISA
3
E: Fab, heavy chain
F: Fab, light chain


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-23 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.420, 100.094, 170.226
Angle α, β, γ (deg.)90.00, 131.82, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 47560.367 Da / Num. of mol.: 2 / Fragment: unp residues 17-460 / Mutation: E148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: clcA, eriC, yadQ, b0155, JW5012 / Production host: Escherichia coli (E. coli) / References: UniProt: P37019
#2: Antibody Fab, heavy chain / Fragment antigen-binding


Mass: 23823.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: MUS MUSCULUS (house mouse)
#3: Antibody Fab, light chain / Fragment antigen-binding


Mass: 23088.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: MUS MUSCULUS (house mouse)
#4: Chemical
ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: F

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG400, 50mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→25 Å / Num. all: 71808 / Num. obs: 71781 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→25 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 34.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 3618 5.04 %random
Rwork0.2485 ---
obs0.2506 71781 99 %-
all-71808 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13215 0 4 0 13219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113543
X-RAY DIFFRACTIONf_angle_d1.01418426
X-RAY DIFFRACTIONf_dihedral_angle_d15.0474762
X-RAY DIFFRACTIONf_chiral_restr0.0632121
X-RAY DIFFRACTIONf_plane_restr0.0052312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7859-2.82250.4121920.38572049X-RAY DIFFRACTION79
2.8225-2.86120.38331410.35042657X-RAY DIFFRACTION100
2.8612-2.9020.3871490.33642598X-RAY DIFFRACTION100
2.902-2.94520.40861570.32182622X-RAY DIFFRACTION100
2.9452-2.99120.40841330.3312611X-RAY DIFFRACTION100
2.9912-3.04010.38851630.32332624X-RAY DIFFRACTION100
3.0401-3.09250.35261420.31072623X-RAY DIFFRACTION100
3.0925-3.14860.4051260.31562651X-RAY DIFFRACTION100
3.1486-3.2090.29671480.29752614X-RAY DIFFRACTION100
3.209-3.27440.3881470.30242628X-RAY DIFFRACTION100
3.2744-3.34540.40911200.30082649X-RAY DIFFRACTION100
3.3454-3.42310.33421440.3052622X-RAY DIFFRACTION100
3.4231-3.50840.34161300.29052677X-RAY DIFFRACTION100
3.5084-3.6030.29611460.27832622X-RAY DIFFRACTION100
3.603-3.70870.32371540.28532635X-RAY DIFFRACTION100
3.7087-3.8280.32481310.26952616X-RAY DIFFRACTION100
3.828-3.96430.30581490.26722647X-RAY DIFFRACTION100
3.9643-4.12240.29771110.25912680X-RAY DIFFRACTION100
4.1224-4.30910.28881280.24142655X-RAY DIFFRACTION100
4.3091-4.5350.2881530.22352643X-RAY DIFFRACTION100
4.535-4.81730.29191420.222640X-RAY DIFFRACTION100
4.8173-5.18620.2581280.21632679X-RAY DIFFRACTION100
5.1862-5.70250.24631490.22392649X-RAY DIFFRACTION100
5.7025-6.5150.3111420.23012682X-RAY DIFFRACTION100
6.515-8.16070.2341340.20522689X-RAY DIFFRACTION100
8.1607-25.0430.22411590.2162701X-RAY DIFFRACTION99

+
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