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- PDB-1rk4: Crystal Structure of a Soluble Dimeric Form of Oxidised CLIC1 -

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Basic information

Entry
Database: PDB / ID: 1rk4
TitleCrystal Structure of a Soluble Dimeric Form of Oxidised CLIC1
ComponentsCHLORIDE INTRACELLULAR CHANNEL PROTEIN 1
KeywordsION TRANSPORT/MEMBRANE PROTEIN / GLUTATHIONE-S-TRANFERASE SUPERFAMILY / CHLORIDE ION CHANNEL / REDOX-CONTROLLED STRUCTURAL TRANSITION / ION TRANSPORT-MEMBRANE PROTEIN COMPLEX
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 / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsLittler, D.R. / Harrop, S.J. / Fairlie, W.D. / Brown, L.J. / Pankhurst, G.J. / Pankhurst, S. / DeMaere, M.Z. / Campbell, T.J. / Bauskin, A.R. / Tonini, R. ...Littler, D.R. / Harrop, S.J. / Fairlie, W.D. / Brown, L.J. / Pankhurst, G.J. / Pankhurst, S. / DeMaere, M.Z. / Campbell, T.J. / Bauskin, A.R. / Tonini, R. / Mazzanti, M. / Breit, S.N. / Curmi, P.M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Intracellular Chloride Ion Channel Protein CLIC1 Undergoes a Redox-controlled Structural Transition
Authors: Littler, D.R. / Harrop, S.J. / Fairlie, W.D. / Brown, L.J. / Pankhurst, G.J. / Pankhurst, S. / DeMaere, M.Z. / Campbell, T.J. / Bauskin, A.R. / Tonini, R. / Mazzanti, M. / Breit, S.N. / Curmi, P.M.
History
DepositionNov 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)54,1942
Polymers54,1942
Non-polymers00
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-17 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.861, 69.189, 107.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1 / Nuclear chloride ion channel 27 / NCC27 / p64 CLCP / Chloride channel ABP / p64CLCP / chloride channel ABP


Mass: 27096.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIC1, NCC27 / Plasmid: PGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O00299
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: PEG MME 5000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.6 mg/mlprotein1drop
214 %(w/v)PEG5000 MME1reservoir
30.1 %sodium acetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Jul 1, 2001 / Details: mirrors
RadiationMonochromator: RIGAKU MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→57.74 Å / Num. all: 40766 / Num. obs: 38677 / % possible obs: 95.6 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 18.53
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 40808 / % possible obs: 95.3 % / Num. measured all: 163232
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 85.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K0M

1k0m


Resolution: 1.792→57.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.593 / SU ML: 0.081 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21324 2089 5.1 %RANDOM
Rwork0.17571 ---
all0.17765 38677 --
obs0.17765 38677 95.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.997 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.792→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 0 342 3661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213392
X-RAY DIFFRACTIONr_bond_other_d0.0020.023064
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9784607
X-RAY DIFFRACTIONr_angle_other_deg0.88537168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5275416
X-RAY DIFFRACTIONr_chiral_restr0.0960.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023742
X-RAY DIFFRACTIONr_gen_planes_other0.010.02658
X-RAY DIFFRACTIONr_nbd_refined0.2250.2748
X-RAY DIFFRACTIONr_nbd_other0.240.23474
X-RAY DIFFRACTIONr_nbtor_other0.0860.21988
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.235
X-RAY DIFFRACTIONr_mcbond_it1.141.52096
X-RAY DIFFRACTIONr_mcangle_it2.04623395
X-RAY DIFFRACTIONr_scbond_it3.0631296
X-RAY DIFFRACTIONr_scangle_it5.0524.51212
LS refinement shellResolution: 1.792→1.839 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 135
Rwork0.223 2490
Refinement
*PLUS
Rfactor Rfree: 0.228 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.44

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