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- PDB-2ja3: Cytoplasmic Domain of the Human Chloride Transporter ClC-5 in com... -

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Basic information

Entry
Database: PDB / ID: 2ja3
TitleCytoplasmic Domain of the Human Chloride Transporter ClC-5 in complex with ADP
ComponentsCHLORIDE CHANNEL PROTEIN 5
KeywordsTRANSPORT PROTEIN / MEMBRANE / CHLORIDE / TRANSPORT / CBS DOMAIN / CLC / CHLORIDE CHANNEL / DISEASE MUTATION / IONIC CHANNEL / ION TRANSPORT / TRANSMEMBRANE / CHLORIDE TRANSPORTER / VOLTAGE-GATED CHANNEL
Function / homology
Function and homology information


renal system process / voltage-gated chloride channel activity / antiporter activity / chloride transport / monoatomic ion transmembrane transport / Stimuli-sensing channels / endocytosis / synaptic vesicle / apical part of cell / early endosome ...renal system process / voltage-gated chloride channel activity / antiporter activity / chloride transport / monoatomic ion transmembrane transport / Stimuli-sensing channels / endocytosis / synaptic vesicle / apical part of cell / early endosome / endosome membrane / lysosomal membrane / Golgi membrane / Golgi apparatus / ATP binding / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
CBS-domain - #20 / Chloride channel ClC-5 / CBS domain Like - #20 / CBS domain Like / CBS-domain / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. ...CBS-domain - #20 / Chloride channel ClC-5 / CBS domain Like - #20 / CBS domain Like / CBS-domain / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / H(+)/Cl(-) exchange transporter 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.05 Å
AuthorsMeyer, S. / Savaresi, S. / Forster, I.C. / Dutzler, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Nucleotide Recognition by the Cytoplasmic Domain of the Human Chloride Transporter Clc-5
Authors: Meyer, S. / Savaresi, S. / Forster, I.C. / Dutzler, R.
History
DepositionNov 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHLORIDE CHANNEL PROTEIN 5
B: CHLORIDE CHANNEL PROTEIN 5
C: CHLORIDE CHANNEL PROTEIN 5
D: CHLORIDE CHANNEL PROTEIN 5
E: CHLORIDE CHANNEL PROTEIN 5
F: CHLORIDE CHANNEL PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,02212
Polymers126,4596
Non-polymers2,5636
Water0
1
A: CHLORIDE CHANNEL PROTEIN 5
B: CHLORIDE CHANNEL PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0074
Polymers42,1532
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CHLORIDE CHANNEL PROTEIN 5
D: CHLORIDE CHANNEL PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0074
Polymers42,1532
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: CHLORIDE CHANNEL PROTEIN 5
F: CHLORIDE CHANNEL PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0074
Polymers42,1532
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.567, 149.308, 81.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31B
41D
12C
22A
13E
23A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A589 - 647
2116C589 - 647
3116B589 - 647
4116D589 - 647
1216A677 - 729
2216C677 - 729
3216B677 - 729
4216D677 - 729
1121C648 - 654
2121A648 - 654
1131E648 - 654
2131A648 - 654

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.577, -0.1521, 0.8024), (-0.1699, -0.9387, -0.3), (0.7989, -0.3094, 0.5158)10.63, 136.8, 21.48
2given(-0.7062, 0.5611, 0.4319), (0.596, 0.1418, 0.7904), (0.3822, 0.8155, -0.4345)-2.852, -19.01, 28.27
3given(-0.9835, -0.1807, -0.004752), (-0.134, 0.7468, -0.6514), (0.1213, -0.6401, -0.7587)75.88, 59.81, 142
4given(-0.7211, 0.5599, 0.408), (0.5501, 0.1048, 0.8285), (0.4211, 0.8219, -0.3836)-0.6677, -17.46, 23.77
5given(-0.5222, -0.1744, 0.8348), (-0.1097, -0.957, -0.2685), (0.8457, -0.2318, 0.4806)9.822, 135.3, 17.03

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Components

#1: Protein
CHLORIDE CHANNEL PROTEIN 5 / / CHLORIDE TRANSPORTER CLC-5 / CLC-5


Mass: 21076.469 Da / Num. of mol.: 6 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 571-746
Source method: isolated from a genetically manipulated source
Details: CHAIN F IS LESS WELL DEFINED WHEN COMPARED TO THE OTHER CHAINS. THIS IS DUE TO MISSING CRYSTAL CONTACTS AND IS REFLECTED IN PARTLY HIGH B-FACTORS.
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EPITHELIUM / Organ: KIDNEY / Plasmid: PET 28 B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51795
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Sequence detailsCONSTRUCT ENCOMPASSES AMINO ACIDS 568 TO 741 OF CLC-5.

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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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growDetails: 200 MM (NH4)2SO4, 10 MM TRIS HCL (PH 7.4) AND 18 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91924
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91924 Å / Relative weight: 1
ReflectionResolution: 2.01→27.56 Å / Num. obs: 45674 / % possible obs: 93.7 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 78.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.1
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.98 / % possible all: 64.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
TRUNCATEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.05→19.83 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.845 / Cross valid method: THROUGHOUT / ESU R Free: 0.558
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PREDOMINANT OLIGOMERIC STATE OF THE CLC- 5 CYTOPLASMIC DOMAIN IN SOLUTION IS A DIMER. CURRENTLY THERE IS NO EXPERIMENTAL EVIDENCE FOR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PREDOMINANT OLIGOMERIC STATE OF THE CLC- 5 CYTOPLASMIC DOMAIN IN SOLUTION IS A DIMER. CURRENTLY THERE IS NO EXPERIMENTAL EVIDENCE FOR THE CORRECT DIMER ARRANGEMENT. A PUTATIVE ARRANGEMENT IS THE PAIR OF CHAINS AB, CD AND EF RELATED BY TWO-FOLD SYMMETRY IN THE ASYMMETRIC UNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1439 5.1 %RANDOM
Rwork0.278 ---
obs0.28 26547 93.8 %-
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: 63.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20 Å2
2---1.58 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 3.05→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8003 0 162 0 8165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228309
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9482.02111314
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3435997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.32123.467323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52151509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2071566
X-RAY DIFFRACTIONr_chiral_restr0.0570.21409
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025913
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.33196
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.55800
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.334
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.56625067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00438369
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.29123242
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.48332945
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21C57tight positional0.440.05
31E57tight positional0.110.05
11A890loose positional0.5120
12C890loose positional0.5220
13B890loose positional0.6520
14D890loose positional0.5220
11A890loose thermal5.2950
12C890loose thermal3.7950
13B890loose thermal2.7450
14D890loose thermal1.9650
21C57loose thermal4.1850
31E57loose thermal8.7850
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 56
Rwork0.366 1267

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