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- PDB-4kkb: Structure of the E148A mutant of CLC-ec1 deltaNC construct in 20m... -

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Basic information

Entry
Database: PDB / ID: 4kkb
TitleStructure of the E148A mutant of CLC-ec1 deltaNC construct in 20mM 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 / immunoglobulin complex / proton transmembrane transport / chloride transmembrane transport / adaptive immune response / extracellular region / 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 / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ig heavy chain V region T601 / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.021 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 1.3Nov 6, 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: 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 area6950 Å2
ΔGint-43 kcal/mol
Surface area30630 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 area3610 Å2
ΔGint-23 kcal/mol
Surface area19590 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 area3650 Å2
ΔGint-23 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.718, 97.533, 170.568
Angle α, β, γ (deg.)90.00, 131.75, 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 / 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) / References: UniProt: P01808*PLUS
#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: 3.81 Å3/Da / Density % sol: 67.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26% PEG400, 100mM Na/K tartrate, 50mM hepes, pH 7.0, 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: 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: 3.02→30 Å / Num. all: 107715 / Num. obs: 107647 / % 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: 3.021→29.734 Å / SU ML: 0.35 / σ(F): 1.91 / σ(I): 2 / Phase error: 31.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 2787 5.06 %random
Rwork0.2363 ---
obs0.2379 107647 98.59 %-
all-107715 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.021→29.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13215 0 0 0 13215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513543
X-RAY DIFFRACTIONf_angle_d0.80518426
X-RAY DIFFRACTIONf_dihedral_angle_d13.7084762
X-RAY DIFFRACTIONf_chiral_restr0.0512121
X-RAY DIFFRACTIONf_plane_restr0.0042312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0208-3.05510.42121170.34212164X-RAY DIFFRACTION62
3.0551-3.0910.35361640.3313381X-RAY DIFFRACTION100
3.091-3.12870.33692010.33323459X-RAY DIFFRACTION100
3.1287-3.16830.32461710.3133506X-RAY DIFFRACTION100
3.1683-3.20990.35511610.30063442X-RAY DIFFRACTION100
3.2099-3.25380.31382050.30823442X-RAY DIFFRACTION100
3.2538-3.30030.31951950.29143411X-RAY DIFFRACTION100
3.3003-3.34940.37831890.29243483X-RAY DIFFRACTION100
3.3494-3.40170.33371720.29473518X-RAY DIFFRACTION100
3.4017-3.45740.30361810.28243401X-RAY DIFFRACTION100
3.4574-3.51690.34861650.28983448X-RAY DIFFRACTION100
3.5169-3.58080.32641530.27673528X-RAY DIFFRACTION100
3.5808-3.64950.32091860.27513445X-RAY DIFFRACTION100
3.6495-3.72390.28151650.26913442X-RAY DIFFRACTION100
3.7239-3.80470.321930.26693498X-RAY DIFFRACTION100
3.8047-3.8930.31950.26033418X-RAY DIFFRACTION100
3.893-3.99020.3132120.25253378X-RAY DIFFRACTION100
3.9902-4.09780.30091990.24733448X-RAY DIFFRACTION100
4.0978-4.2180.23771580.23993499X-RAY DIFFRACTION100
4.218-4.35380.2642040.22523430X-RAY DIFFRACTION100
4.3538-4.50890.24981990.20873435X-RAY DIFFRACTION100
4.5089-4.68870.23462030.20963452X-RAY DIFFRACTION100
4.6887-4.90120.20841660.20213450X-RAY DIFFRACTION100
4.9012-5.15840.24561920.20923441X-RAY DIFFRACTION100
5.1584-5.47970.22881890.20353468X-RAY DIFFRACTION100
5.4797-5.89970.26481880.20673433X-RAY DIFFRACTION100
5.8997-6.48790.25671750.20993487X-RAY DIFFRACTION100
6.4879-7.4140.20451960.19923450X-RAY DIFFRACTION100
7.414-9.29320.19091540.17633456X-RAY DIFFRACTION100
9.2932-29.73590.28711970.25623389X-RAY DIFFRACTION98

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