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- PDB-4kjw: Structure of the CLC-ec1 deltaNC construct in 100mM fluoride and ... -

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Basic information

Entry
Database: PDB / ID: 4kjw
TitleStructure of the CLC-ec1 deltaNC construct in 100mM fluoride and 20mM bromide
Components
  • Fab, heavy chain
  • Fab, light chain
  • H(+)/Cl(-) exchange transporter ClcA
KeywordsTRANSPORT PROTEIN / membrane protein / membrane transporter
Function / homology
Function and homology information


cellular stress response to acidic pH / chloride:proton antiporter activity / voltage-gated chloride channel activity / proton transmembrane transport / chloride transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsLim, H.-H. / Miller, C.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Fluoride-dependent interruption of the transport cycle of a CLC Cl(-)/H(+) antiporter.
Authors: Lim, H.H. / Stockbridge, R.B. / Miller, C.
History
DepositionMay 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA
C: Fab, heavy chain
D: Fab, light chain
E: Fab, heavy chain
F: Fab, light chain


Theoretical massNumber of molelcules
Total (without water)189,0606
Polymers189,0606
Non-polymers00
Water00
1
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA


Theoretical massNumber of molelcules
Total (without water)95,2372
Polymers95,2372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-45 kcal/mol
Surface area30620 Å2
MethodPISA
2
C: Fab, heavy chain
D: Fab, light chain


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-21 kcal/mol
Surface area19740 Å2
MethodPISA
3
E: Fab, heavy chain
F: Fab, light chain


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-22 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.681, 98.892, 172.908
Angle α, β, γ (deg.)90.00, 132.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H(+)/Cl(-) exchange transporter ClcA / ClC-ec1


Mass: 47618.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0155, clcA, eriC, JW5012, yadQ / Production host: Escherichia coli (E. coli) / References: UniProt: P37019
#2: Antibody Fab, heavy chain


Mass: 23823.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: MUS MUSCULUS (house mouse)
#3: Antibody Fab, light chain


Mass: 23088.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: MUS MUSCULUS (house mouse)
Has protein modificationY

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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: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 25% PEG400, 100mM Na/K tartrate, 100mM Glycine, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 3.03→40 Å / Num. all: 108501 / Num. obs: 108408 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.101
Reflection shellResolution: 3.03→3.1 Å / Rmerge(I) obs: 0.612

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ENE

4ene


Resolution: 3.03→39.485 Å / SU ML: 0.39 / σ(F): 1.93 / Phase error: 30.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 2819 5.08 %random
Rwork0.2298 ---
obs0.2318 52698 98.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.03→39.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13223 0 0 0 13223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513551
X-RAY DIFFRACTIONf_angle_d0.80318436
X-RAY DIFFRACTIONf_dihedral_angle_d13.7844768
X-RAY DIFFRACTIONf_chiral_restr0.052121
X-RAY DIFFRACTIONf_plane_restr0.0042314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.025-3.05940.33971240.32142260X-RAY DIFFRACTION66
3.0594-3.09540.47841740.33893564X-RAY DIFFRACTION100
3.0954-3.13310.35871850.34113407X-RAY DIFFRACTION100
3.1331-3.17270.34312060.31583492X-RAY DIFFRACTION100
3.1727-3.21450.30671920.29183461X-RAY DIFFRACTION100
3.2145-3.25850.36151870.29763444X-RAY DIFFRACTION100
3.2585-3.3050.32281780.29123531X-RAY DIFFRACTION100
3.305-3.35430.3131750.27623400X-RAY DIFFRACTION100
3.3543-3.40670.28441810.28193570X-RAY DIFFRACTION100
3.4067-3.46250.36781850.26333406X-RAY DIFFRACTION100
3.4625-3.52220.25531910.25523488X-RAY DIFFRACTION100
3.5222-3.58620.2931880.24443489X-RAY DIFFRACTION100
3.5862-3.65510.30781950.25653457X-RAY DIFFRACTION100
3.6551-3.72970.25431650.24343446X-RAY DIFFRACTION100
3.7297-3.81070.29292020.24223501X-RAY DIFFRACTION100
3.8107-3.89930.311730.24333460X-RAY DIFFRACTION100
3.8993-3.99670.29382210.23333444X-RAY DIFFRACTION100
3.9967-4.10470.25731910.23213482X-RAY DIFFRACTION100
4.1047-4.22530.27291980.2153453X-RAY DIFFRACTION100
4.2253-4.36150.23531860.2083478X-RAY DIFFRACTION100
4.3615-4.51720.22271940.2013464X-RAY DIFFRACTION100
4.5172-4.69780.22221860.20163483X-RAY DIFFRACTION100
4.6978-4.91120.24181700.18923452X-RAY DIFFRACTION100
4.9112-5.16960.22751970.20143465X-RAY DIFFRACTION100
5.1696-5.49270.26751950.20483485X-RAY DIFFRACTION100
5.4927-5.91550.2661480.20683517X-RAY DIFFRACTION100
5.9155-6.50840.25321860.21093454X-RAY DIFFRACTION100
6.5084-7.44470.24111770.20173486X-RAY DIFFRACTION100
7.4447-9.35890.1911770.17433466X-RAY DIFFRACTION100
9.3589-39.48790.30521840.26863392X-RAY DIFFRACTION97

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