[English] 日本語
Yorodumi
- PDB-3kjy: Crystal structure of reduced HOMO SAPIENS CLIC3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kjy
TitleCrystal structure of reduced HOMO SAPIENS CLIC3
ComponentsChloride intracellular channel protein 3Chloride channel
KeywordsTRANSPORT PROTEIN / GST / GLUTATHIONE / CLIC / CHLORIDE CHANNEL / CHLORIDE INTRACEL / CHLORIDE / CYTOPLASM / ION TRANSPORT / IONIC CHANNEL / NUCLEUS / POLYMORPHISM / TRANSPORT / VOLTAGE-GATED CHANNEL
Function / homology
Function and homology information


chloride transport / chloride channel activity / chloride channel complex / nuclear body / signal transduction / extracellular exosome / membrane / nucleus / cytoplasm
Similarity search - Function
Intracellular chloride channel / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Intracellular chloride channel / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chloride intracellular channel protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLittler, D.R. / Curmi, P.M.G. / Breit, S.N. / Perrakis, A.
CitationJournal: Proteins / Year: 2010
Title: Structure of human CLIC3 at 2 A resolution
Authors: Littler, D.R. / Brown, L.J. / Breit, S.N. / Perrakis, A. / Curmi, P.M.G.
History
DepositionNov 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chloride intracellular channel protein 3
B: Chloride intracellular channel protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1259
Polymers56,4522
Non-polymers6727
Water2,630146
1
A: Chloride intracellular channel protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7076
Polymers28,2261
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chloride intracellular channel protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4183
Polymers28,2261
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.080, 48.380, 59.760
Angle α, β, γ (deg.)69.68, 80.89, 74.60
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Chloride intracellular channel protein 3 / Chloride channel


Mass: 28226.191 Da / Num. of mol.: 2 / Fragment: UNP residues 1-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIC3 / Plasmid: PET-28-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O95833
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Solution (15mg/ml protein in 20mm HEPES-NAOH, PH 7.5, 200mm NACl) plus 3 micro-l of reservoir solutionl (0.95M NH4SO4,0.225M LISO4, 0.1M TRIS-HCL PH 8.5), drop equilibrated against 1 ml ...Details: Solution (15mg/ml protein in 20mm HEPES-NAOH, PH 7.5, 200mm NACl) plus 3 micro-l of reservoir solutionl (0.95M NH4SO4,0.225M LISO4, 0.1M TRIS-HCL PH 8.5), drop equilibrated against 1 ml reservoir solution , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, CRYO Reservoir + 20%V Ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 3, 2009 / Details: Osmic-mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→30.26 Å / Num. obs: 32724 / % possible obs: 92.5 % / Redundancy: 2.2 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.048 / Net I/σ(I): 15.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.553 / % possible all: 89.4

-
Processing

Software
NameVersionClassification
AMoREphasing
PHENIX(phenix.refine: 1.4_161)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FY7

3fy7


Resolution: 1.95→30.26 Å / SU ML: 0.32 / σ(F): 0.02 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 1548 5.06 %
Rwork0.1978 --
obs0.2003 30567 86.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.385 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso mean: 41.87 Å2
Baniso -1Baniso -2Baniso -3
1--4.949 Å2-0.598 Å24.717 Å2
2---0.018 Å2-0.983 Å2
3---4.967 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 35 146 3719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073643
X-RAY DIFFRACTIONf_angle_d1.0214941
X-RAY DIFFRACTIONf_dihedral_angle_d16.4191358
X-RAY DIFFRACTIONf_chiral_restr0.069548
X-RAY DIFFRACTIONf_plane_restr0.005645
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.01970.34051100.2843245972
2.0197-2.10060.30181260.2377260378
2.1006-2.19610.28031520.2029282384
2.1961-2.31190.26131470.1959283584
2.3119-2.45670.26751580.1928283985
2.4567-2.64620.25511670.1923296788
2.6462-2.91230.24781700.1968298490
2.9123-3.33330.25311400.2147311892
3.3333-4.19780.22871730.1665319395
4.1978-30.26310.20562050.1782319896
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4843-2.2686-2.45453.78594.36365.14720.4959-0.82570.9189-0.34670.1086-0.2352-0.5680.3808-0.50230.2434-0.05070.09180.297-0.19150.3275-22.236614.969826.1987
26.2758-3.11910.0755.85491.04193.63360.2891-1.71591.5742-0.32280.2101-1.32360.02470.2195-0.44930.1848-0.05520.01320.5297-0.3230.5149-11.54489.796530.3342
32.36880.50160.24131.609-0.06870.26280.02070.8531-0.1073-0.48310.0027-0.236-0.00030.307-0.04870.2927-0.00720.04210.4004-0.03110.1372.1737-0.1449-12.479
41.94170.7865-1.10531.8806-1.14471.27920.14260.93810.163-0.3692-0.03250.78080.2531-0.8936-0.0360.28790.0562-0.07810.5774-0.06540.1897-9.651-2.0948-14.6233
51.659-0.0443-1.15620.60020.41342.48130.0906-0.0297-0.13770.1883-0.09610.1665-0.039-0.06830.01610.10960.0022-0.02760.04070.01780.185-4.6222-4.740611.7316
61.6777-0.11030.13550.08860.12281.79670.07140.185-0.31170.04210.0193-0.15440.09240.2287-0.06630.11110.0104-0.00870.1189-0.02310.15415.1492-3.29254.6774
70.31880.2228-0.06980.8305-0.10220.45730.3725-0.45560.00120.1459-0.20470.08310.36990.17610.02350.3970.17840.04440.7508-0.19880.23627.1026-4.1167-19.2997
81.5808-0.4128-0.59491.26840.67732.1333-0.06440.06840.04350.2060.3023-0.21930.19050.2032-0.18240.37890.0650.10840.6751-0.29780.3634-26.626216.169334.8048
91.7466-0.7635-1.50861.4110.61432.21690.10680.1278-0.1452-0.2032-0.0465-0.28680.1255-0.0085-0.07260.0954-0.0142-0.03520.10420.00540.1629-19.3326-2.91188.9181
102.5455-0.0993-0.49180.46970.09672.00260.14720.08580.21740.07010.0260.0404-0.2391-0.3654-0.15180.09150.0323-0.00750.09790.03340.1284-27.17394.841512.9335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and ((resseq 5:45))B0
2X-RAY DIFFRACTION2chain 'B' and ((resseq 59:89))B0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 4:45))A0
4X-RAY DIFFRACTION4chain 'A' and ((resseq 56:90))A0
5X-RAY DIFFRACTION5chain 'A' and ((resseq 91:159))A0
6X-RAY DIFFRACTION6chain 'A' and ((resseq 160:230))A0
7X-RAY DIFFRACTION7chain 'A' and ((resseq -8:-3))A0
8X-RAY DIFFRACTION8chain 'B' and ((resseq -9:-3))B0
9X-RAY DIFFRACTION9chain 'B' and ((resseq 90:159))B0
10X-RAY DIFFRACTION10chain 'B' and ((resseq 160:230))B0

+
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