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- PDB-4kka: Structure of the E148A mutant of CLC-ec1 deltaNC construct in 100... -

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Basic information

Entry
Database: PDB / ID: 4kka
TitleStructure of the E148A mutant of 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 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 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 5, 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 1.3Oct 16, 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

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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)188,9446
Polymers188,9446
Non-polymers00
Water00
1
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA


Theoretical massNumber of molelcules
Total (without water)95,1212
Polymers95,1212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-42 kcal/mol
Surface area30640 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 area3650 Å2
ΔGint-22 kcal/mol
Surface area19660 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 area3580 Å2
ΔGint-23 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.338, 99.339, 170.290
Angle α, β, γ (deg.)90.00, 131.94, 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: 47560.367 Da / Num. of mol.: 2 / Fragment: CLC-ec1 deltaNC, unp residues 17-460 / Mutation: E148A
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: 3.85 Å3/Da / Density % sol: 68.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 24% PEG400, 100mM Na/K tartrate, 50mM 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→40 Å / Num. all: 112390 / Num. obs: 112322 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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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 / Resolution: 3→39.848 Å / SU ML: 0.46 / σ(F): 1.94 / σ(I): 2 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2818 4.93 %random
Rwork0.2202 ---
obs0.2223 112322 99.31 %-
all-112390 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→39.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13206 0 0 0 13206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113534
X-RAY DIFFRACTIONf_angle_d1.28318414
X-RAY DIFFRACTIONf_dihedral_angle_d15.914758
X-RAY DIFFRACTIONf_chiral_restr0.0792120
X-RAY DIFFRACTIONf_plane_restr0.0062310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9974-3.10450.38155000.305510099X-RAY DIFFRACTION94
3.1045-3.22880.33425330.291310790X-RAY DIFFRACTION100
3.2288-3.37560.35456460.272710677X-RAY DIFFRACTION100
3.3756-3.55350.32815550.252710769X-RAY DIFFRACTION100
3.5535-3.7760.30385590.229610733X-RAY DIFFRACTION100
3.776-4.06730.24885530.212110748X-RAY DIFFRACTION100
4.0673-4.47610.25196560.194310643X-RAY DIFFRACTION100
4.4761-5.12260.25745390.198810753X-RAY DIFFRACTION100
5.1226-6.44960.22995080.193910831X-RAY DIFFRACTION100
6.4496-39.85150.21734850.216510745X-RAY DIFFRACTION99

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