- PDB-2ja3: Cytoplasmic Domain of the Human Chloride Transporter ClC-5 in com... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2ja3
Title
Cytoplasmic Domain of the Human Chloride Transporter ClC-5 in complex with ADP
Components
CHLORIDE CHANNEL PROTEIN 5
Keywords
TRANSPORT 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
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
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.91924 Å / Relative weight: 1
Reflection
Resolution: 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 shell
Resolution: 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
Name
Version
Classification
REFMAC
5.2.0019
refinement
DENZO
datareduction
TRUNCATE
datascaling
Refinement
Method 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.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.317
1439
5.1 %
RANDOM
Rwork
0.278
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obs
0.28
26547
93.8 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK