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- PDB-7f8r: Crystal structure of human soluble CLIC1 with catalytic cysteine ... -

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Basic information

Entry
Database: PDB / ID: 7f8r
TitleCrystal structure of human soluble CLIC1 with catalytic cysteine (Cys24) in sulphonic acid form.
ComponentsChloride intracellular channel protein 1
KeywordsOXIDOREDUCTASE / human / Chloride Intracellular Channel 1 / CLIC1 / Cysteine sulfonic acid
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 / nuclear membrane / vesicle ...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 / 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, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Chloride intracellular channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsKumar, A. / Das, B.K. / Sreeshma, N.S. / Arockiasamy, A.
Funding support India, 3items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR28080/BID/7/836/20/18 India
Department of Biotechnology (DBT, India)BT/PR28766/BRB/10/1701/2018 India
Department of Science & Technology (DST, India)EMR/2017/005066 India
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Comparative kinetic analysis of ascorbate (Vitamin-C) recycling dehydroascorbate reductases from plants and humans.
Authors: Das, B.K. / Kumar, A. / Sreekumar, S.N. / Ponraj, K. / Gadave, K. / Kumar, S. / Murali Achary, V.M. / Ray, P. / Reddy, M.K. / Arockiasamy, A.
History
DepositionJul 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)54,0012
Polymers54,0012
Non-polymers00
Water1,49583
1
A: Chloride intracellular channel protein 1


Theoretical massNumber of molelcules
Total (without water)27,0011
Polymers27,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chloride intracellular channel protein 1


Theoretical massNumber of molelcules
Total (without water)27,0011
Polymers27,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.020, 70.655, 82.412
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chloride intracellular channel protein 1 / 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: 27000.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIC1, G6, NCC27 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00299
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 45.86 % / Description: Cubic crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.02M Sodium potassium phosphate, 0.1M Bis-Tris propane pH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.503→82.412 Å / Num. obs: 16309 / % possible obs: 97.2 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.035 / Rrim(I) all: 0.071 / Net I/σ(I): 16.2 / Num. measured all: 66696
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.503-2.54940.44232568150.8970.2490.5093.294
6.869-82.4123.70.02930238140.9990.0170.03437.197.4

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Processing

Software
NameVersionClassification
XDSFeb 5, 2021 (BUILT 20210323)data reduction
autoPROC0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
PHENIX1.16-3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K0M

1k0m


Resolution: 2.51→42.06 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.518 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.258 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 795 4.9 %RANDOM
Rwork0.1752 ---
obs0.1781 15396 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.52 Å2 / Biso mean: 43.751 Å2 / Biso min: 21.34 Å2
Baniso -1Baniso -2Baniso -3
1--3.69 Å20 Å20.58 Å2
2--5.46 Å20 Å2
3----1.77 Å2
Refinement stepCycle: final / Resolution: 2.51→42.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 0 83 3723
Biso mean---40.52 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133714
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173445
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.6525051
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5738020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9824.066182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44415620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3311515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
LS refinement shellResolution: 2.511→2.576 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 71 -
Rwork0.237 1093 -
all-1164 -
obs--95.8 %

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