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- PDB-6erz: The crystal structure of mouse chloride intracellular channel pro... -

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Basic information

Entry
Database: PDB / ID: 6erz
TitleThe crystal structure of mouse chloride intracellular channel protein 6
ComponentsChloride intracellular channel protein 6
KeywordsTRANSPORT PROTEIN / CLIC / GST / Glutathione Transferase / Ion channel / CHLORIDE CHANNEL
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors / chloride channel activity / chloride channel complex / oxidoreductase activity / plasma membrane / cytoplasm
Similarity search - Function
Intracellular chloride channel / : / CLIC-like 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, C-terminal domain superfamily ...Intracellular chloride channel / : / CLIC-like 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / 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 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.923 Å
AuthorsFerofontov, A. / Giladi, M. / Haitin, Y.
CitationJournal: Sci Rep / Year: 2018
Title: Inherent flexibility of CLIC6 revealed by crystallographic and solution studies.
Authors: Ferofontov, A. / Strulovich, R. / Marom, M. / Giladi, M. / Haitin, Y.
History
DepositionOct 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloride intracellular channel protein 6
B: Chloride intracellular channel protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6088
Polymers54,0052
Non-polymers6026
Water4,071226
1
A: Chloride intracellular channel protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3174
Polymers27,0031
Non-polymers3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chloride intracellular channel protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2914
Polymers27,0031
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.384, 51.637, 101.101
Angle α, β, γ (deg.)90.000, 119.620, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 and (name N or name...
21(chain B and (resid 3 through 9 or (resid 10...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(chain A and ((resid 3 and (name N or name...AA33
12METMETLYSLYS(chain A and ((resid 3 and (name N or name...AA3 - 2383 - 238
13METMETLYSLYS(chain A and ((resid 3 and (name N or name...AA3 - 2383 - 238
14METMETLYSLYS(chain A and ((resid 3 and (name N or name...AA3 - 2383 - 238
15METMETLYSLYS(chain A and ((resid 3 and (name N or name...AA3 - 2383 - 238
21METMETVALVAL(chain B and (resid 3 through 9 or (resid 10...BB3 - 93 - 9
22LYSLYSALAALA(chain B and (resid 3 through 9 or (resid 10...BB10 - 1110 - 11
23METMETARGARG(chain B and (resid 3 through 9 or (resid 10...BB3 - 2363 - 236
24METMETARGARG(chain B and (resid 3 through 9 or (resid 10...BB3 - 2363 - 236
25METMETARGARG(chain B and (resid 3 through 9 or (resid 10...BB3 - 2363 - 236
26METMETARGARG(chain B and (resid 3 through 9 or (resid 10...BB3 - 2363 - 236

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Components

#1: Protein Chloride intracellular channel protein 6


Mass: 27002.738 Da / Num. of mol.: 2 / Fragment: residues 363-596
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clic6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BHB9
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, LiSO4, Bis-Tris

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.82→46.975 Å / Num. obs: 47963 / % possible obs: 98.5 % / Redundancy: 6.39 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.66

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XSCALEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHE

2ahe


Resolution: 1.923→46.975 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.39
RfactorNum. reflection% reflection
Rfree0.2491 1718 5 %
Rwork0.2033 --
obs0.2056 34378 83.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.64 Å2 / Biso mean: 49.3548 Å2 / Biso min: 23.33 Å2
Refinement stepCycle: final / Resolution: 1.923→46.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 45 226 3641
Biso mean--96.94 50.06 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083473
X-RAY DIFFRACTIONf_angle_d0.8954739
X-RAY DIFFRACTIONf_chiral_restr0.053542
X-RAY DIFFRACTIONf_plane_restr0.007614
X-RAY DIFFRACTIONf_dihedral_angle_d10.2892054
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1915X-RAY DIFFRACTION8.697TORSIONAL
12B1915X-RAY DIFFRACTION8.697TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9228-1.97940.7894160.6993023189
1.9794-2.04320.4692550.43961052110733
2.0432-2.11630.38091140.33582173228767
2.1163-2.2010.35211580.33243018317693
2.201-2.30120.35741700.30173217338799
2.3012-2.42250.31861710.25663249342099
2.4225-2.57430.29771690.25313222339199
2.5743-2.7730.29141710.23873236340799
2.773-3.0520.29841710.22933264343599
3.052-3.49350.25171720.1923263343599
3.4935-4.4010.17581740.151433183492100
4.401-46.98850.21411770.16453346352399
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)
17.4868-0.5472-0.17392.6890.10275.4234-0.2588-0.7462-0.05190.50450.06230.29990.1873-0.71680.14170.28770.07960.04430.3563-0.0280.277142.823742.02426.0214
24.00450.6562-1.4946.3743-0.80667.8125-0.263-1.40850.76180.41060.03130.5832-0.2611-1.03560.14010.51150.2507-0.01290.7557-0.14730.452940.281749.655332.2197
32.2805-0.2163-0.23260.28470.02720.5337-0.2377-0.02790.2110.1510.11910.1637-0.1213-0.1770.11510.37490.0892-0.07320.314-0.03020.462535.003748.507410.3135
41.7284-0.61340.59622.08811.04622.0594-0.1344-0.1854-0.11670.05370.00420.30540.0029-0.27090.10630.19630.02380.0040.24-0.01070.299137.893939.6967.0868
53.78270.91130.75411.8778-0.41372.73220.0304-0.5150.0810.3037-0.05610.0679-0.07890.00760.03960.38230.11980.01670.3605-0.00450.276659.051435.791931.5105
66.5591.2586-1.43163.0287-2.01735.9427-0.1917-2.0087-0.19271.3594-0.12920.0876-0.3473-0.11340.34590.86850.07790.01761.10430.10410.593260.507431.036444.6415
71.80530.6509-0.65392.10880.75765.2494-0.3405-0.4226-0.52370.30890.04670.10350.3606-0.25660.25760.52530.0790.02340.36650.09370.38456.55724.083226.4446
81.4563-0.2575-0.2721.26740.06462.31-0.1419-0.52060.01890.4620.3225-0.45690.37710.4607-0.25450.42460.2274-0.13920.4656-0.05750.426283.662732.713323.9947
97.73221.1466-3.56183.8947-1.6375.0527-0.67740.4733-0.405-0.29570.2629-0.22540.8354-0.2420.41490.3306-0.00910.04730.2464-0.02530.282472.009229.51545.6103
104.90533.77280.45337.16211.30543.1661-0.0462-0.47720.18610.2853-0.0171-0.29160.12910.2890.11080.3650.1382-0.08290.3078-0.05130.330974.690238.637825.9768
111.5096-0.4931-0.96351.6371-0.3751.9534-0.0213-0.22060.26620.22820.1017-0.2056-0.13350.2946-0.0510.3320.0656-0.05640.2946-0.05690.323873.690542.486523.2702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 43 )A3 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 73 )A44 - 73
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 142 )A74 - 142
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 238 )A143 - 238
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 43 )B3 - 43
6X-RAY DIFFRACTION6chain 'B' and (resid 44 through 62 )B44 - 62
7X-RAY DIFFRACTION7chain 'B' and (resid 63 through 97 )B63 - 97
8X-RAY DIFFRACTION8chain 'B' and (resid 98 through 142 )B98 - 142
9X-RAY DIFFRACTION9chain 'B' and (resid 143 through 171 )B143 - 171
10X-RAY DIFFRACTION10chain 'B' and (resid 172 through 192 )B172 - 192
11X-RAY DIFFRACTION11chain 'B' and (resid 193 through 236 )B193 - 236

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