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- PDB-3fy7: Crystal structure of homo sapiens CLIC3 -

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Basic information

Entry
Database: PDB / ID: 3fy7
TitleCrystal structure of homo sapiens CLIC3
ComponentsChloride intracellular channel protein 3Chloride channel
KeywordsTRANSPORT PROTEIN / GST / GLUTATHIONE / CLIC / CHLORIDE CHANNEL / CHLORIDE INTRACEL / Chloride / Ion transport / Ionic channel / Nucleus / Transport / Voltage-gated channel
Function / homology
Function and homology information


chloride transport / chloride channel activity / chloride channel complex / nuclear body / signal transduction / extracellular exosome / membrane / nucleus / cytoplasm
Similarity search - Function
Intracellular chloride channel / Glutathione S-transferase, 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Intracellular chloride channel / Glutathione S-transferase, 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 / Soluble glutathione S-transferase N-terminal domain profile. / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLittler, D.R. / Curmi, P.M.G. / Breit, S.N. / Perrakis, A.
CitationJournal: Proteins / Year: 2010
Title: Structure of human CLIC3 at 2 A resolution
Authors: Littler, D.R. / Brown, L.J. / Breit, S.N. / Perrakis, A. / Curmi, P.M.G.
History
DepositionJan 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Nov 1, 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 3
B: Chloride intracellular channel protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8376
Polymers56,4522
Non-polymers3844
Water2,504139
1
A: Chloride intracellular channel protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4183
Polymers28,2261
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Chloride intracellular channel protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4183
Polymers28,2261
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.289, 48.673, 60.154
Angle α, β, γ (deg.)69.11, 80.97, 74.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Chloride intracellular channel protein 3 / Chloride channel


Mass: 28226.191 Da / Num. of mol.: 2 / Fragment: UNP residues 1-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIC3 / Plasmid: pET-28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O95833
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: SOLUTION (15 MG/ML PROTEIN IN 20 MM HEPES*NAOH, PH 7.5, 200MM NACL) PLUS 3UL OF RESERVOIR SOLUTION (1.05M NH4SO4,0.225M LISO4, 0.1M TRIS-HCL PH 8.5), DROP EQUILIBRATED AGAINST 1 ML RESERVOIR ...Details: SOLUTION (15 MG/ML PROTEIN IN 20 MM HEPES*NAOH, PH 7.5, 200MM NACL) PLUS 3UL OF RESERVOIR SOLUTION (1.05M NH4SO4,0.225M LISO4, 0.1M TRIS-HCL PH 8.5), DROP EQUILIBRATED AGAINST 1 ML RESERVOIR SOLUTION , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→28.3 Å / Num. obs: 33742 / % possible obs: 94 % / Redundancy: 1.9 % / Biso Wilson estimate: 24.86 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.122 / Net I/σ(I): 8.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4518 / Rsym value: 0.656 / % possible all: 86.6

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Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AHE

2ahe


Resolution: 1.95→28.03 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.876 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 12.488 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1697 5 %RANDOM
Rwork0.231 32041 --
obs0.234 33738 93.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.85 Å2 / Biso mean: 13.401 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0.04 Å20.08 Å2
2---0.08 Å2-0.07 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 20 139 3663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213670
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.984985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7565444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85923.149181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14915611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2251532
X-RAY DIFFRACTIONr_chiral_restr0.0740.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212832
X-RAY DIFFRACTIONr_mcbond_it0.5651.52238
X-RAY DIFFRACTIONr_mcangle_it0.95423610
X-RAY DIFFRACTIONr_scbond_it1.68731432
X-RAY DIFFRACTIONr_scangle_it2.6084.51375
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 109 -
Rwork0.312 1982 -
all-2091 -
obs--79.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.23610.4831-0.63161.9710.08053.0042-0.04740.3474-0.1842-0.17810.0804-0.1044-0.01740.0186-0.0330.04460.0051-0.01530.0822-0.01880.0785-0.2838-3.0950.8743
22.63630.0884-0.32662.19940.84293.34320.1482-0.16850.17140.04550.0034-0.0159-0.1755-0.131-0.15160.03880.01660.00690.07470.02820.0615-21.58055.313217.6392
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-17 - 230
2X-RAY DIFFRACTION2B-17 - 230

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