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

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Basic information

Entry
Database: PDB / ID: 6ery
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: 1.795 Å
AuthorsFerofontov, A. / Giladi, M. / Haitin, Y.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel
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 1.1Jan 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
B: Chloride intracellular channel protein 6
A: Chloride intracellular channel protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2945
Polymers54,0052
Non-polymers2883
Water5,549308
1
B: Chloride intracellular channel protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1953
Polymers27,0031
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chloride intracellular channel protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0992
Polymers27,0031
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.623, 68.989, 80.980
Angle α, β, γ (deg.)90.000, 95.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 361 through 367 or (resid 368...
21(chain B and ((resid 361 and (name N or name...

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
11METMETVALVAL(chain A and (resid 361 through 367 or (resid 368...AB361 - 3673 - 9
12LYSLYSLYSLYS(chain A and (resid 361 through 367 or (resid 368...AB36810
13METMETARGARG(chain A and (resid 361 through 367 or (resid 368...AB361 - 5943 - 236
14METMETARGARG(chain A and (resid 361 through 367 or (resid 368...AB361 - 5943 - 236
15METMETARGARG(chain A and (resid 361 through 367 or (resid 368...AB361 - 5943 - 236
16METMETARGARG(chain A and (resid 361 through 367 or (resid 368...AB361 - 5943 - 236
17METMETARGARG(chain A and (resid 361 through 367 or (resid 368...AB361 - 5943 - 236
21METMETMETMET(chain B and ((resid 361 and (name N or name...BA3613
22GLYGLYLYSLYS(chain B and ((resid 361 and (name N or name...BA359 - 5961 - 238
23GLYGLYLYSLYS(chain B and ((resid 361 and (name N or name...BA359 - 5961 - 238
24GLYGLYLYSLYS(chain B and ((resid 361 and (name N or name...BA359 - 5961 - 238
25GLYGLYLYSLYS(chain B and ((resid 361 and (name N or name...BA359 - 5961 - 238

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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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
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: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→40.327 Å / Num. obs: 50630 / % possible obs: 98.8 % / Redundancy: 5.23 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.82
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.955 / Mean I/σ(I) obs: 0.42 / Num. unique all: 3274 / % possible all: 87.4

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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: 1.795→40.327 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.45
RfactorNum. reflection% reflection
Rfree0.2196 1884 5 %
Rwork0.1813 --
obs0.1832 37676 86.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.29 Å2 / Biso mean: 38.9645 Å2 / Biso min: 15.63 Å2
Refinement stepCycle: final / Resolution: 1.795→40.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 15 308 3868
Biso mean--133.51 43.47 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083643
X-RAY DIFFRACTIONf_angle_d0.9064962
X-RAY DIFFRACTIONf_chiral_restr0.054557
X-RAY DIFFRACTIONf_plane_restr0.007649
X-RAY DIFFRACTIONf_dihedral_angle_d2.6072586
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1960X-RAY DIFFRACTION12.124TORSIONAL
12B1960X-RAY DIFFRACTION12.124TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.795-1.84350.2896160.320930331910
1.8435-1.89780.2975570.26881085114234
1.8978-1.9590.32561300.26742463259377
1.959-2.02910.31680.254231883356100
2.0291-2.11030.26491650.238131473312100
2.1103-2.20630.27381670.23131653332100
2.2063-2.32260.25931680.199831973365100
2.3226-2.46810.23961670.186831783345100
2.4681-2.65870.25031690.188732073376100
2.6587-2.92610.26351670.183931723339100
2.9261-3.34940.20981690.186132173386100
3.3494-4.21920.17631690.148832113380100
4.2192-40.33710.1751720.15263259343199
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)
11.8657-1.1311-0.58054.6538-0.01915.6246-0.00240.58390.2559-0.459-0.0399-0.616-0.19220.8344-0.0220.31460.01270.12850.33140.06620.3159-13.63118.248-24.7614
25.1508-0.15540.62193.02890.65993.4366-0.12090.31640.5406-0.35160.067-0.1599-0.57570.21890.03850.2446-0.01430.00930.22090.0350.2169-18.39257.5833-21.147
39.0045-1.0605-0.83828.15846.99286.624-0.38430.97820.218-0.0442-0.61781.0217-0.5656-0.940.56030.39590.0208-0.02560.3150.02210.2664-26.012711.0828-25.8225
44.35735.3704-2.07336.7922-1.20748.56060.1132-0.64950.87420.3905-0.12420.9852-0.635-0.31970.14160.24630.08590.00320.309-0.03440.3051-29.62348.584-17.0368
52.45242.49292.62114.20553.31693.7266-0.0753-0.27430.198-0.0221-0.17050.0296-0.3018-0.24710.25460.21420.0284-0.01430.18480.02420.2066-21.02679.368-5.8324
69.00036.68110.29845.46261.34623.50990.4417-0.42630.41350.7934-0.3743-0.0757-0.2890.1808-0.07590.3815-0.0526-0.06950.26890.00260.2848-12.04315.18166.7938
75.8078-3.02162.05164.0436-4.11814.89060.11450.6621-0.58330.35950.34761.301-0.35940.4294-0.41890.4212-0.14670.01260.5058-0.0460.3704-26.9762-6.77178.2497
81.4851-0.0748-1.19391.86640.14372.14890.125-0.2874-0.10710.4403-0.2879-0.25770.16590.21990.13360.2627-0.0785-0.05680.2990.03490.1933-15.6252.4512-0.8901
91.43670.27250.35972.96770.98492.728-0.0070.09280.08070.18930.0132-0.4392-0.1080.46190.00110.1841-0.0272-0.03470.29490.04710.2936-7.29315.8699-4.6673
103.36190.4421-1.12783.9216-0.44872.71750.0369-0.17010.0778-0.0629-0.01-0.5383-0.01920.5225-0.02040.1441-0.0196-0.01410.2649-0.00810.18821.016524.718725.5443
111.49180.384-0.49172.9462-0.11382.19310.0054-0.0645-0.15360.3727-0.03960.13820.42090.04940.01620.29370.0205-0.00450.21050.02570.1597-10.30597.234431.0863
122.6968-0.3153-0.33364.71730.2432.5760.06520.2881-0.1886-0.3915-0.0402-0.10280.36590.0627-0.01080.29810.0144-0.02740.2789-0.04360.1586-8.02076.447518.9411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 359 through 379 )B359 - 379
2X-RAY DIFFRACTION2chain 'B' and (resid 380 through 420 )B380 - 420
3X-RAY DIFFRACTION3chain 'B' and (resid 421 through 431 )B421 - 431
4X-RAY DIFFRACTION4chain 'B' and (resid 432 through 442 )B432 - 442
5X-RAY DIFFRACTION5chain 'B' and (resid 443 through 477 )B443 - 477
6X-RAY DIFFRACTION6chain 'B' and (resid 478 through 500 )B478 - 500
7X-RAY DIFFRACTION7chain 'B' and (resid 501 through 510 )B501 - 510
8X-RAY DIFFRACTION8chain 'B' and (resid 511 through 550 )B511 - 550
9X-RAY DIFFRACTION9chain 'B' and (resid 551 through 596 )B551 - 596
10X-RAY DIFFRACTION10chain 'A' and (resid 361 through 424 )A361 - 424
11X-RAY DIFFRACTION11chain 'A' and (resid 425 through 550 )A425 - 550
12X-RAY DIFFRACTION12chain 'A' and (resid 551 through 594 )A551 - 594

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