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- PDB-2d2z: Crystal structure of Soluble Form Of CLIC4 -

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Basic information

Entry
Database: PDB / ID: 2d2z
TitleCrystal structure of Soluble Form Of CLIC4
ComponentsChloride intracellular channel protein 4Chloride channel
KeywordsTRANSPORT PROTEIN / Soluble Form / CLIC4
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: 2.2 Å
AuthorsLi, Y.F. / Li, D.F. / Wang, D.C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Trimeric structure of the wild soluble chloride intracellular ion channel CLIC4 observed in crystals
Authors: Li, Y.F. / Li, D.F. / Zeng, Z.H. / Wang, D.C.
History
DepositionSep 21, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Chloride intracellular channel protein 4
C: Chloride intracellular channel protein 4


Theoretical massNumber of molelcules
Total (without water)89,6413
Polymers89,6413
Non-polymers00
Water13,763764
1
A: Chloride intracellular channel protein 4


Theoretical massNumber of molelcules
Total (without water)29,8801
Polymers29,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chloride intracellular channel protein 4


Theoretical massNumber of molelcules
Total (without water)29,8801
Polymers29,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chloride intracellular channel protein 4


Theoretical massNumber of molelcules
Total (without water)29,8801
Polymers29,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.190, 86.050, 73.380
Angle α, β, γ (deg.)90.00, 112.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29880.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET 22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y696
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium citrate, ethanol, Magnesium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 2, 2004
RadiationMonochromator: con-focus / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→23.49 Å / Num. obs: 43497 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 7.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 17.7 / Num. unique all: 6195 / Rsym value: 0.365 / % possible all: 99.7

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Processing

Software
NameVersionClassification
crystalcleardata collection
SCALAdata scaling
CCP4model building
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→23.49 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 4285 -random
Rwork0.216 ---
obs0.216 42522 99.7 %-
all-42641 --
Displacement parametersBiso mean: 38.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→23.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5474 0 0 764 6238
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.374 717 -
Rwork0.313 --
obs-6319 99.9 %

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