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- PDB-3o3t: Crystal Structure Analysis of M32A mutant of human CLIC1 -

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Basic information

Entry
Database: PDB / ID: 3o3t
TitleCrystal Structure Analysis of M32A mutant of human CLIC1
ComponentsChloride intracellular channel protein 1
KeywordsTRANSPORT PROTEIN / CLIC / Glutathione Transferase / thioredoxin / ion channel / domain interface
Function / homology
Function and homology information


glutathione dehydrogenase (ascorbate) / Oxidoreductases; Acting on a sulfur group of donors / chloride transport / chloride channel activity / brush border / chloride channel complex / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope ...glutathione dehydrogenase (ascorbate) / Oxidoreductases; Acting on a sulfur group of donors / chloride transport / chloride channel activity / brush border / chloride channel complex / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope / nuclear membrane / vesicle / blood microparticle / oxidoreductase activity / 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 / : / CLIC-like 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 / Glutathione S-transferase, C-terminal-like ...Chloride intracellular channel protein 1 / Intracellular chloride channel / : / CLIC-like 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsFanucchi, S. / Achilonu, I.A. / Adamson, R.J. / Fernandes, M.A. / Stoychev, S. / Dirr, H.W.
CitationJournal: To be Published
Title: Crystal Structure Analysis of M32A mutant of human CLIC1
Authors: Fanucchi, S. / Stoychev, S.H. / Achilonu, I.A. / Adamson, R. / Fernandes, M.A. / Dirr, H.W.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
SupersessionSep 8, 2010ID: 3MA4
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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 1


Theoretical massNumber of molelcules
Total (without water)26,8931
Polymers26,8931
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.360, 63.985, 82.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26892.566 Da / Num. of mol.: 1 / Mutation: M32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIC1, 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


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% (w/v) PEG 3350, 0.1M Tris-HCl, 0.2M sodium acetate pH 7.5, 0.02% azide, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 5, 2009 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→50.63 Å / Num. obs: 25911 / % possible obs: 98.59 % / Redundancy: 5.24 % / Rsym value: 0.148 / Net I/σ(I): 166.319
Reflection shell
Resolution (Å)Rsym value
1.59-1.6470.657
1.647-1.7130.607
1.713-1.7910.505
1.791-1.8850.361
1.885-2.0030.234
2.003-2.1580.181
2.158-2.3750.179
2.375-2.7190.178
2.719-3.4260.155
3.426-50.630.115

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.48 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å50.63 Å
Translation2.5 Å50.63 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 30027
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.59-10028.40.722508
5.16-6.5930.10.85505
4.44-5.1627.60.873556
3.95-4.44250.887613
3.6-3.9521.70.869685
3.32-3.626.30.854729
3.1-3.3226.10.846788
2.92-3.129.10.825841
2.77-2.9228.10.838883
2.64-2.7728.20.847918
2.52-2.6426.30.86977
2.42-2.5227.70.8611005
2.33-2.4228.70.8531046
2.25-2.33270.8591072
2.18-2.2527.40.8561120
2.12-2.18290.8681144
2.06-2.12280.8521188
2-2.0629.90.8421220
1.95-232.40.821234
1.9-1.9532.50.8271284
1.86-1.937.10.7961305
1.82-1.8634.90.8181337
1.78-1.8234.80.8011339
1.74-1.7837.80.7631403
1.71-1.7438.90.7451419
1.68-1.7140.50.7521443
1.65-1.6842.70.7191456
1.6-1.6546.60.6352009

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Processing

Software
NameVersionClassificationNB
SAINTV7.34Adata scaling
PHASER2.1.4phasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50.63 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.2208 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7754 / SU B: 7.608 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1395 / SU Rfree: 0.1349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1293 5.1 %RANDOM
Rwork0.2292 ---
obs0.2313 25462 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.89 Å2 / Biso mean: 17.4453 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 0 150 2001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221889
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9832563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33525.11686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31815326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.648159
X-RAY DIFFRACTIONr_chiral_restr0.1370.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211425
X-RAY DIFFRACTIONr_mcbond_it0.3351.51180
X-RAY DIFFRACTIONr_mcangle_it0.80921906
X-RAY DIFFRACTIONr_scbond_it2.2323709
X-RAY DIFFRACTIONr_scangle_it3.5944.5657
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 93 -
Rwork0.334 1758 -
all-1851 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.232 Å / Origin y: 1.802 Å / Origin z: 16.3 Å
111213212223313233
T0.1321 Å2-0.0089 Å2-0.0045 Å2-0.1936 Å20.0088 Å2--0.0213 Å2
L1.2836 °2-0.2392 °20.0604 °2-0.5134 °20.0338 °2--1.1706 °2
S-0.0094 Å °0.017 Å °0.0371 Å °-0.0195 Å °0.0038 Å °-0.0116 Å °-0.0139 Å °0.0401 Å °0.0056 Å °

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