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- PDB-1k0m: Crystal structure of a soluble monomeric form of CLIC1 at 1.4 ang... -

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Basic information

Entry
Database: PDB / ID: 1k0m
TitleCrystal structure of a soluble monomeric form of CLIC1 at 1.4 angstroms
ComponentsCHLORIDE INTRACELLULAR CHANNEL PROTEIN 1
KeywordsMETAL TRANSPORT / glutathione-S-tranferase superfamily / Chloride Ion Channel
Function / homology
Function and homology information


glutathione dehydrogenase (ascorbate) / Oxidoreductases; Acting on a sulfur group of donors / chloride transport / chloride channel activity / brush border / chloride channel complex / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope ...glutathione dehydrogenase (ascorbate) / Oxidoreductases; Acting on a sulfur group of donors / chloride transport / chloride channel activity / brush border / chloride channel complex / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope / nuclear membrane / blood microparticle / vesicle / oxidoreductase activity / cadherin binding / perinuclear region of cytoplasm / endoplasmic reticulum / signal transduction / mitochondrion / extracellular space / extracellular exosome / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Chloride intracellular channel protein 1 / Intracellular chloride channel / : / CLIC-like 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 / Glutathione S-transferase, C-terminal-like ...Chloride intracellular channel protein 1 / Intracellular chloride channel / : / CLIC-like 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 / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.4 Å
AuthorsHarrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. ...Harrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. / Bauskin, A.R. / Wu, W.M. / Pankhurst, S. / Campbell, T.J. / Breit, S.N. / Curmi, P.M.G.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of a soluble form of the intracellular chloride ion channel CLIC1 (NCC27) at 1.4-A resolution.
Authors: Harrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. / Bauskin, A.R. / Wu, W.M. / Pankhurst, S. / ...Authors: Harrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. / Bauskin, A.R. / Wu, W.M. / Pankhurst, S. / Campbell, T.J. / Breit, S.N. / Curmi, P.M.
History
DepositionSep 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1
B: CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)53,7632
Polymers53,7632
Non-polymers00
Water11,818656
1
A: CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)26,8821
Polymers26,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)26,8821
Polymers26,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.271, 55.332, 89.140
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211
DetailsSOLUBLE MONOMERIC FORM

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Components

#1: Protein CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1 / CLIC1 / NCC27


Mass: 26881.605 Da / Num. of mol.: 2 / Fragment: CLIC1 / Mutation: E151G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00299
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG MME 5K, AMMONIUM SULPHATE, SODIUM ACETATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-20 mg/mlprotein1drop
20.5 %n-octyl-beta-D-glucopyranoside1drop
314-18 %PEG5000 MME1reservoir
40-30 mMammonium sulfate1reservoir
50.1 Msodium acetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998 / Details: MONOCHROMATOR
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→87 Å / Num. all: 81905 / Num. obs: 81905 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.022 / Rsym value: 0.022 / Net I/σ(I): 28.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 9.3 / Num. unique all: 4039 / Rsym value: 0.098 / % possible all: 94.2
Reflection
*PLUS
Lowest resolution: 87 Å / Num. obs: 81729 / % possible obs: 94.1 % / Num. measured all: 259290 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 94 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 6.5

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.4→87.71 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: TLS parameters refined for the N and C domains in each monomer
RfactorNum. reflection% reflectionSelection details
Rfree0.17799 4089 5 %RANDOM
Rwork0.13815 ---
all0.14012 77616 --
obs0.14012 77616 94.69 %-
Displacement parametersBiso mean: 10.755 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.24 Å2
2--0.96 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.4→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 0 656 4378
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0181.598
X-RAY DIFFRACTIONp_angle_d1.772.4
LS refinement shellHighest resolution: 1.4 Å / Rfactor Rfree: 0.177 / Rfactor Rwork: 0.127 / Total num. of bins used: 20
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.772.4

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