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- PDB-4jzq: Crystal structure of human CLIC1 C24D mutant -

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Basic information

Entry
Database: PDB / ID: 4jzq
TitleCrystal structure of human CLIC1 C24D mutant
ComponentsChloride intracellular channel protein 1Chloride channel
KeywordsTRANSPORT PROTEIN / CLIC / Glutathione-S-Transferase fold / Chloride ion channel
Function / homology
Function and homology information


chloride transport / chloride channel activity / brush border / chloride channel complex / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope / blood microparticle / nuclear membrane ...chloride transport / chloride channel activity / brush border / chloride channel complex / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope / blood microparticle / nuclear membrane / vesicle / cadherin binding / perinuclear region of cytoplasm / endoplasmic reticulum / signal transduction / mitochondrion / extracellular space / extracellular exosome / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Chloride intracellular channel protein 1 / 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 ...Chloride intracellular channel protein 1 / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPhang, J.M. / Harrop, S.J. / Duff, A.P. / Wilk, K.E. / Curmi, P.M.G.
CitationJournal: To be Published
Title: Crystal structure analysis of CLIC1 C24 mutants
Authors: Phang, J.M. / Harrop, S.J. / Duff, A.P. / Wilk, K.E. / Curmi, P.M.G.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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 1
B: Chloride intracellular channel protein 1


Theoretical massNumber of molelcules
Total (without water)54,2182
Polymers54,2182
Non-polymers00
Water12,881715
1
A: Chloride intracellular channel protein 1


Theoretical massNumber of molelcules
Total (without water)27,1091
Polymers27,1091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chloride intracellular channel protein 1


Theoretical massNumber of molelcules
Total (without water)27,1091
Polymers27,1091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.381, 69.691, 83.420
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chloride intracellular channel protein 1 / Chloride channel / Chloride channel ABP / Nuclear chloride ion channel 27 / NCC27 / Regulatory nuclear chloride ion ...Chloride channel ABP / Nuclear chloride ion channel 27 / NCC27 / Regulatory nuclear chloride ion channel protein / hRNCC


Mass: 27108.760 Da / Num. of mol.: 2 / Fragment: CLIC1 / Mutation: C24D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIC1, CLIC1 G6 NCC27, G6, NCC27 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00299
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2% Tacsimate, 0.1M Bis-Tris, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95363
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2010
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95363 Å / Relative weight: 1
ReflectionResolution: 1.35→53.48 Å / Num. all: 99542 / Num. obs: 99542 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 3.6 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 12.1
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3.3 / Num. unique all: 10480 / Rsym value: 0.265 / % possible all: 67.6

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K0M

1k0m


Resolution: 1.35→27.807 Å / SU ML: 0.18 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Phase error: 16.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1821 4980 5 %Random
Rwork0.1511 ---
obs0.1527 99509 93.5 %-
all-99509 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.078 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2076 Å20 Å2-0.3233 Å2
2--3.9482 Å20 Å2
3----1.7164 Å2
Refinement stepCycle: LAST / Resolution: 1.35→27.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 0 715 4424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153906
X-RAY DIFFRACTIONf_angle_d1.5275326
X-RAY DIFFRACTIONf_dihedral_angle_d13.4521505
X-RAY DIFFRACTIONf_chiral_restr0.097600
X-RAY DIFFRACTIONf_plane_restr0.01707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.39830.30683670.25666453X-RAY DIFFRACTION64
1.3983-1.45420.26754550.21848115X-RAY DIFFRACTION81
1.4542-1.52040.20215170.15369752X-RAY DIFFRACTION97
1.5204-1.60060.16634920.12459937X-RAY DIFFRACTION98
1.6006-1.70080.16675140.1139987X-RAY DIFFRACTION99
1.7008-1.83210.17485180.12379971X-RAY DIFFRACTION99
1.8321-2.01650.17865450.14019994X-RAY DIFFRACTION99
2.0165-2.30810.16675070.145810054X-RAY DIFFRACTION100
2.3081-2.90750.17225410.152910162X-RAY DIFFRACTION100
2.9075-27.81260.1855240.161310104X-RAY DIFFRACTION98

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