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- PDB-2ahe: Crystal structure of a soluble form of CLIC4. intercellular chlor... -

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Basic information

Entry
Database: PDB / ID: 2ahe
TitleCrystal structure of a soluble form of CLIC4. intercellular chloride ion channel
ComponentsChloride intracellular channel protein 4Chloride channel
KeywordsMETAL TRANSPORT / Glutathione-S-transferase superfamily / CLIC4 / NCC27 / chloride ion channel
Function / homology
Function and homology information


establishment or maintenance of apical/basal cell polarity / retina vasculature morphogenesis in camera-type eye / endothelial cell morphogenesis / vacuolar acidification / fertilization / chloride transport / regulation of cytoskeleton organization / chloride channel activity / branching morphogenesis of an epithelial tube / microvillus ...establishment or maintenance of apical/basal cell polarity / retina vasculature morphogenesis in camera-type eye / endothelial cell morphogenesis / vacuolar acidification / fertilization / chloride transport / regulation of cytoskeleton organization / chloride channel activity / branching morphogenesis of an epithelial tube / microvillus / chloride channel complex / keratinocyte differentiation / cellular response to calcium ion / negative regulation of cell migration / multicellular organism growth / cytoplasmic vesicle membrane / nuclear matrix / cell-cell junction / actin cytoskeleton / apical part of cell / midbody / angiogenesis / cell differentiation / centrosome / perinuclear region of cytoplasm / cell surface / mitochondrion / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Intracellular chloride channel / 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, N-terminal / Glutathione S-transferase, C-terminal domain superfamily ...Intracellular chloride channel / 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, 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLittler, D.R. / Assaad, N.N. / Harrop, S.J. / Brown, L.J. / Pankhurst, G.J. / Luciani, P. / Aguilar, M.-I. / Mazzanti, M. / Berryman, M.A. / Breit, S.N. / Curmi, P.M.G.
CitationJournal: FEBS J. / Year: 2005
Title: Crystal structure of the soluble form of the redox-regulated chloride ion channel protein CLIC4.
Authors: Littler, D.R. / Assaad, N.N. / Harrop, S.J. / Brown, L.J. / Pankhurst, G.J. / Luciani, P. / Aguilar, M.-I. / Mazzanti, M. / Berryman, M.A. / Breit, S.N. / Curmi, P.M.G.
History
DepositionJul 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chloride intracellular channel protein 4


Theoretical massNumber of molelcules
Total (without water)30,3531
Polymers30,3531
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.717, 79.478, 42.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Chloride intracellular channel protein 4 / Chloride channel / Intracellular chloride ion channel protein p64H1


Mass: 30352.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y696
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.17 Å3/Da / Density % sol: 43.21 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 22, 2003 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→55.9 Å / Num. all: 25137 / Num. obs: 25137 / % possible obs: 99.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.65 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 8.3584
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.56 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.3 / Num. unique all: 3600 / Rsym value: 0.58 / % possible all: 99.87

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KOM

1kom
PDB Unreleased entry


Resolution: 1.8→24.62 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.623 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22941 1281 5.1 %RANDOM
Rwork0.19446 ---
all0.19618 23815 --
obs0.19618 23815 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 0 196 2016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221861
X-RAY DIFFRACTIONr_bond_other_d0.0010.021711
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9912518
X-RAY DIFFRACTIONr_angle_other_deg0.85534020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74124.68479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37315342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.571159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02349
X-RAY DIFFRACTIONr_nbd_refined0.2240.2383
X-RAY DIFFRACTIONr_nbd_other0.1780.21659
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2925
X-RAY DIFFRACTIONr_nbtor_other0.0840.21006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4271.51478
X-RAY DIFFRACTIONr_mcbond_other0.2981.5450
X-RAY DIFFRACTIONr_mcangle_it1.67721867
X-RAY DIFFRACTIONr_scbond_it3.053838
X-RAY DIFFRACTIONr_scangle_it4.2084.5651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 114 -
Rwork0.255 1720 -
obs--100 %

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