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- PDB-2yv7: Crystal structure of the CLIC homolog from drosophila melanogaster -

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Basic information

Entry
Database: PDB / ID: 2yv7
TitleCrystal structure of the CLIC homolog from drosophila melanogaster
ComponentsCG10997-PA
KeywordsMETAL TRANSPORT / CLIC / DmCLIC / CHLORIDE ION CHANNEL / GST FOLD
Function / homology
Function and homology information


negative gravitaxis / response to alcohol / glutathione peroxidase / glutathione peroxidase activity / chloride transport / chloride channel activity / lipid binding / calcium ion binding / mitochondrion / nucleoplasm ...negative gravitaxis / response to alcohol / glutathione peroxidase / glutathione peroxidase activity / chloride transport / chloride channel activity / lipid binding / calcium ion binding / mitochondrion / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
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 domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Chloride intracellular channel, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHarrop, S.J. / Littler, D.R. / Curmi, P.M.G.
CitationJournal: Proteins / Year: 2007
Title: Comparison of vertebrate and invertebrate CLIC proteins: The crystal structures of Caenorhabditis elegans EXC-4 and Drosophila melanogaster DmCLIC
Authors: Littler, D.R. / Harrop, S.J. / Brown, L.J. / Pankhurst, G.J. / Mynott, A.V. / Luciani, P. / Mandyam, R.A. / Mazzanti, M. / Tanda, S. / Berryman, M.A. / Breit, S.N. / Curmi, P.M.G.
History
DepositionApr 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG10997-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3763
Polymers30,2091
Non-polymers1672
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.393, 63.451, 114.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CG10997-PA / LD46306p / CLIC


Mass: 30208.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VY78
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% PEG 3350, pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 26, 2005
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→57.07 Å / Num. obs: 29963 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 18.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.233 / % possible all: 91.3

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K0M

1k0m


Resolution: 1.7→32 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.088 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1590 5.1 %RANDOM
Rwork0.216 ---
obs0.218 29884 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--1.24 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 2 95 2006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221948
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9752632
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7425232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18624.60789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58415364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.218159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021432
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2916
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21365
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.341192
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.71761912
X-RAY DIFFRACTIONr_scbond_it3.284824
X-RAY DIFFRACTIONr_scangle_it3.5323720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 93 -
Rwork0.258 1876 -
obs--84.43 %

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