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- PDB-4iqa: Crystal Structure Analysis of the E228L Mutant of Human CLIC1 -

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Basic information

Entry
Database: PDB / ID: 4iqa
TitleCrystal Structure Analysis of the E228L Mutant of Human CLIC1
ComponentsChloride intracellular channel protein 1Chloride channel
KeywordsTRANSPORT PROTEIN / CLIC / Glutathione Transferase / pH salt bridge 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
AuthorsCross, M.O. / Achilonu, I.A. / Fernandes, M.A. / Fanucchi, S. / Dirr, H.W.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure Analysis of the E228L Mutant of Human CLIC1
Authors: Cross, M.O. / Fanucchi, S. / Dirr, H.W. / Fernandes, M.A. / Achilonu, I.
History
DepositionJan 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 28, 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
B: Chloride intracellular channel protein 1


Theoretical massNumber of molelcules
Total (without water)52,6962
Polymers52,6962
Non-polymers00
Water0
1
A: Chloride intracellular channel protein 1


Theoretical massNumber of molelcules
Total (without water)26,3481
Polymers26,3481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chloride intracellular channel protein 1


Theoretical massNumber of molelcules
Total (without water)26,3481
Polymers26,3481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.768, 71.938, 83.074
Angle α, β, γ (deg.)90.000, 90.440, 90.000
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: 26348.098 Da / Num. of mol.: 2 / Mutation: E228L
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

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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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NaCl, 0.1 M HEPES 25% (w/v) PEG 3350, 0.02% azide, 5 mM DTT, pH 7.5, 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
ReflectionRedundancy: 11.16 % / Av σ(I) over netI: 19.84 / Number: 192608 / Rsym value: 0.227 / D res high: 2.486 Å / Num. obs: 17255 / % possible obs: 99.02
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRsym value
4.255.3610.215
3.714.2510.225
3.373.7110.236
3.133.3710.236
2.953.1310.243
2.82.9510.247
2.682.810.256
2.582.6810.276
2.492.5810.288
ReflectionResolution: 2.486→36.12 Å / Num. obs: 17255 / % possible obs: 99.02 % / Redundancy: 11.16 % / Rsym value: 0.227 / Net I/σ(I): 19.841
Reflection shell
Resolution (Å)Rsym valueDiffraction-ID
2.486-2.5750.2881
2.575-2.6780.2761
2.678-2.80.2561
2.8-2.9470.2471
2.947-3.1320.2431
3.132-3.3740.2361
3.374-3.7130.2361
3.713-4.2510.2251
4.251-5.3550.2151

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å54.38 Å
Translation2.5 Å54.38 Å

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Processing

Software
NameVersionClassificationNB
SAINTV7.68Adata scaling
SAINTV7.68Adata reduction
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
APEXdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→36.12 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.868 / WRfactor Rfree: 0.2986 / WRfactor Rwork: 0.2407 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7242 / SU B: 32.84 / SU ML: 0.328 / SU R Cruickshank DPI: 0.7503 / SU Rfree: 0.3562 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.75 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3037 867 5 %RANDOM
Rwork0.2455 ---
obs0.2485 17234 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.43 Å2 / Biso mean: 45.4462 Å2 / Biso min: 19.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0.27 Å2
2--0.32 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.49→36.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 0 0 3489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193563
X-RAY DIFFRACTIONr_bond_other_d0.0010.023477
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9864832
X-RAY DIFFRACTIONr_angle_other_deg0.79438018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.34724.615156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26215617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.661518
X-RAY DIFFRACTIONr_chiral_restr0.070.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02781
LS refinement shellResolution: 2.49→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 63 -
Rwork0.273 1086 -
all-1149 -
obs--89 %
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)
10.6010.35590.11220.76470.08350.0511-0.0181-0.01110.0239-0.0480.02590.07910.02130.0428-0.00780.16350.0248-0.01030.07280.00610.137-0.8377-3.814385.1327
21.10560.58590.97710.38750.33854.96510.33990.0088-0.15220.09850.114-0.1370.0619-0.6691-0.45390.2007-0.0350.05310.18390.02110.1654-10.4579-0.0036127.0657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 240
2X-RAY DIFFRACTION2B6 - 240

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