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- PDB-4k0g: Crystal structure of human CLIC1 C24S mutant -

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Basic information

Entry
Database: PDB / ID: 4k0g
TitleCrystal structure of human CLIC1 C24S 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
ACETATE ION / Chloride intracellular channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chloride intracellular channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1773
Polymers28,0781
Non-polymers992
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.215, 82.728, 42.167
Angle α, β, γ (deg.)90.00, 116.43, 90.00
Int Tables number5
Space group name H-MC121

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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: 28077.723 Da / Num. of mol.: 1 / Fragment: CLIC1 / Mutation: C24S
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Calcium acetate hydrate, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 29, 2010
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.4→37.76 Å / Num. all: 49590 / Num. obs: 49590 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 7.2 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 17.9
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.9 / Num. unique all: 49768 / Rsym value: 0.434 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K0M

1k0m


Resolution: 1.4→27.194 Å / SU ML: 0.18 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.37 / σ(I): 0 / Phase error: 15.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1806 2512 5.07 %Random
Rwork0.155 ---
obs0.1563 49588 99.92 %-
all-49588 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.665 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.0145 Å20 Å2-2.3572 Å2
2--2.4402 Å2-0 Å2
3---1.5743 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 5 394 2263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051966
X-RAY DIFFRACTIONf_angle_d0.9542678
X-RAY DIFFRACTIONf_dihedral_angle_d13.345756
X-RAY DIFFRACTIONf_chiral_restr0.064301
X-RAY DIFFRACTIONf_plane_restr0.005356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.28992330.25014692X-RAY DIFFRACTION100
1.45-1.50810.22132290.18694735X-RAY DIFFRACTION100
1.5081-1.57670.21972340.16264730X-RAY DIFFRACTION100
1.5767-1.65980.1862450.14694667X-RAY DIFFRACTION100
1.6598-1.76380.21182620.14134726X-RAY DIFFRACTION100
1.7638-1.90.16022770.13584647X-RAY DIFFRACTION100
1.9-2.09110.16482520.14834709X-RAY DIFFRACTION100
2.0911-2.39350.19932690.15634687X-RAY DIFFRACTION100
2.3935-3.0150.16582770.14924713X-RAY DIFFRACTION100
3.015-27.19920.16322340.15384770X-RAY DIFFRACTION99

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