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- PDB-3kjy: Crystal structure of reduced HOMO SAPIENS CLIC3 -

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Basic information

Entry
Database: PDB / ID: 3kjy
TitleCrystal structure of reduced HOMO SAPIENS CLIC3
ComponentsChloride intracellular channel protein 3
KeywordsTRANSPORT PROTEIN / GST / GLUTATHIONE / CLIC / CHLORIDE CHANNEL / CHLORIDE INTRACEL / CHLORIDE / CYTOPLASM / ION TRANSPORT / IONIC CHANNEL / NUCLEUS / POLYMORPHISM / TRANSPORT / VOLTAGE-GATED CHANNEL
Function / homology
Function and homology information


chloride transport / chloride channel activity / voltage-gated ion channel activity / chloride channel complex / regulation of ion transmembrane transport / nuclear body / signal transduction / extracellular exosome / nucleus / cytoplasm
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal domain / Glutathione Transferase family / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily / Chloride intracellular channel protein 3 / Glutathione S-transferase, N-terminal / Intracellular chloride channel
Chloride intracellular channel protein 3
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)57,1259
Polymers56,4522
Non-polymers6727
Water2,630146
1
A: Chloride intracellular channel protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7076
Polymers28,2261
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Unit cell
γ
α
β
Length a, b, c (Å)48.080, 48.380, 59.760
Angle α, β, γ (deg.)69.68, 80.89, 74.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide Chloride intracellular channel protein 3


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


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Solution (15mg/ml protein in 20mm HEPES-NAOH, PH 7.5, 200mm NACl) plus 3 micro-l of reservoir solutionl (0.95M NH4SO4,0.225M LISO4, 0.1M TRIS-HCL PH 8.5), drop equilibrated against 1 ml reservoir solution , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, CRYO Reservoir + 20%V Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 3, 2009 / Details: Osmic-mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→30.26 Å / Num. obs: 32724 / % possible obs: 92.5 % / Redundancy: 2.2 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.048 / Net I/σ(I): 15.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.553 / % possible all: 89.4

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Processing

Software
NameVersionClassification
AMoREphasing
PHENIX(phenix.refine: 1.4_161)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FY7
Resolution: 1.95→30.26 Å / SU ML: 0.32 / σ(F): 0.02 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 1548 5.06 %
Rwork0.1978 --
Obs0.2003 30567 86.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.385 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso mean: 41.87 Å2
Baniso -1Baniso -2Baniso -3
1--4.949 Å2-0.598 Å24.717 Å2
2---0.018 Å2-0.983 Å2
3---4.967 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 35 146 3719
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0073643
f_angle_d1.0214941
f_dihedral_angle_d16.4191358
f_chiral_restr0.069548
f_plane_restr0.005645
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.01970.34051100.2843245972
2.0197-2.10060.30181260.2377260378
2.1006-2.19610.28031520.2029282384
2.1961-2.31190.26131470.1959283584
2.3119-2.45670.26751580.1928283985
2.4567-2.64620.25511670.1923296788
2.6462-2.91230.24781700.1968298490
2.9123-3.33330.25311400.2147311892
3.3333-4.19780.22871730.1665319395
4.1978-30.26310.20562050.1782319896
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.4843-2.2686-2.45453.78594.36365.14720.4959-0.82570.9189-0.34670.1086-0.2352-0.5680.3808-0.50230.2434-0.05070.09180.297-0.19150.3275-22.236614.969826.1987
26.2758-3.11910.0755.85491.04193.63360.2891-1.71591.5742-0.32280.2101-1.32360.02470.2195-0.44930.1848-0.05520.01320.5297-0.3230.5149-11.54489.796530.3342
32.36880.50160.24131.609-0.06870.26280.02070.8531-0.1073-0.48310.0027-0.236-0.00030.307-0.04870.2927-0.00720.04210.4004-0.03110.1372.1737-0.1449-12.479
41.94170.7865-1.10531.8806-1.14471.27920.14260.93810.163-0.3692-0.03250.78080.2531-0.8936-0.0360.28790.0562-0.07810.5774-0.06540.1897-9.651-2.0948-14.6233
51.659-0.0443-1.15620.60020.41342.48130.0906-0.0297-0.13770.1883-0.09610.1665-0.039-0.06830.01610.10960.0022-0.02760.04070.01780.185-4.6222-4.740611.7316
61.6777-0.11030.13550.08860.12281.79670.07140.185-0.31170.04210.0193-0.15440.09240.2287-0.06630.11110.0104-0.00870.1189-0.02310.15415.1492-3.29254.6774
70.31880.2228-0.06980.8305-0.10220.45730.3725-0.45560.00120.1459-0.20470.08310.36990.17610.02350.3970.17840.04440.7508-0.19880.23627.1026-4.1167-19.2997
81.5808-0.4128-0.59491.26840.67732.1333-0.06440.06840.04350.2060.3023-0.21930.19050.2032-0.18240.37890.0650.10840.6751-0.29780.3634-26.626216.169334.8048
91.7466-0.7635-1.50861.4110.61432.21690.10680.1278-0.1452-0.2032-0.0465-0.28680.1255-0.0085-0.07260.0954-0.0142-0.03520.10420.00540.1629-19.3326-2.91188.9181
102.5455-0.0993-0.49180.46970.09672.00260.14720.08580.21740.07010.0260.0404-0.2391-0.3654-0.15180.09150.0323-0.00750.09790.03340.1284-27.17394.841512.9335
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION / Auth seq-ID: 0

IDRefine TLS-IDSelection detailsAuth asym-ID
11chain 'B' and ((resseq 5:45))B
22chain 'B' and ((resseq 59:89))B
33chain 'A' and ((resseq 4:45))A
44chain 'A' and ((resseq 56:90))A
55chain 'A' and ((resseq 91:159))A
66chain 'A' and ((resseq 160:230))A
77chain 'A' and ((resseq -8:-3))A
88chain 'B' and ((resseq -9:-3))B
99chain 'B' and ((resseq 90:159))B
1010chain 'B' and ((resseq 160:230))B

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