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- PDB-4kjp: Structure of the CLC-ec1 deltaNC construct in the absence of halide -

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Basic information

Entry
Database: PDB / ID: 4kjp
TitleStructure of the CLC-ec1 deltaNC construct in the absence of halide
Components
  • H(+)/Cl(-) exchange transporter ClcA
  • heavy chain of Fab fragment
  • light chain of Fab fragment
Keywordstranport protein / membrane protein / membrane transporting protein
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: 3.2 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 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: heavy chain of Fab fragment
D: light chain of Fab fragment
E: heavy chain of Fab fragment
F: light chain of Fab fragment


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 area6940 Å2
ΔGint-44 kcal/mol
Surface area30580 Å2
MethodPISA
2
C: heavy chain of Fab fragment
D: light chain of Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-22 kcal/mol
Surface area19620 Å2
MethodPISA
3
E: heavy chain of Fab fragment
F: light chain of Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-23 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.449, 98.246, 171.026
Angle α, β, γ (deg.)90.00, 132.08, 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 / Fragment: unp residues 17-460
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 heavy chain of Fab fragment


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


Mass: 23088.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / 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: 3.83 Å3/Da / Density % sol: 67.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 23% PEG400, 100mM K-isethionate, 100 mM 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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. all: 47173 / Num. obs: 47173 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→24.887 Å / SU ML: 0.44 / σ(F): 1.93 / Phase error: 30.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 2382 5.05 %random
Rwork0.2221 ---
obs0.2243 47156 99.14 %-
all-47133 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→24.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13214 0 0 0 13214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613542
X-RAY DIFFRACTIONf_angle_d0.82518424
X-RAY DIFFRACTIONf_dihedral_angle_d13.6264764
X-RAY DIFFRACTIONf_chiral_restr0.0522120
X-RAY DIFFRACTIONf_plane_restr0.0042312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1957-3.26080.37381010.31082376X-RAY DIFFRACTION89
3.2608-3.33150.35931170.29562597X-RAY DIFFRACTION98
3.3315-3.40880.35211410.29422646X-RAY DIFFRACTION100
3.4088-3.49390.3491320.27752644X-RAY DIFFRACTION100
3.4939-3.58810.31661390.25762619X-RAY DIFFRACTION100
3.5881-3.69330.2971510.25862635X-RAY DIFFRACTION100
3.6933-3.81210.34171650.25092627X-RAY DIFFRACTION100
3.8121-3.94790.25431330.23422648X-RAY DIFFRACTION100
3.9479-4.10520.27451600.2272620X-RAY DIFFRACTION100
4.1052-4.29120.25641440.20452646X-RAY DIFFRACTION100
4.2912-4.51620.23821430.19282658X-RAY DIFFRACTION100
4.5162-4.79720.23931460.18892631X-RAY DIFFRACTION100
4.7972-5.16460.2281500.18612652X-RAY DIFFRACTION100
5.1646-5.67870.25261340.19232684X-RAY DIFFRACTION100
5.6787-6.48770.25771400.20972668X-RAY DIFFRACTION100
6.4877-8.12630.19531460.19762683X-RAY DIFFRACTION100
8.1263-24.88760.26621400.23092740X-RAY DIFFRACTION99

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