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- PDB-4kkl: Structure of the E148A mutant of CLC-ec1 delta NC construct in 10... -

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Basic information

Entry
Database: PDB / ID: 4kkl
TitleStructure of the E148A mutant of CLC-ec1 delta NC construct in 100mM fluoride
Components
  • Fab, heavy chain
  • Fab, light chain
  • H(+)/Cl(-) exchange transporter ClcA
Keywordstranport 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
FLUORIDE ION / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsStockbridge, R.B. / Lim, 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 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,02010
Polymers188,9446
Non-polymers764
Water00
1
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1976
Polymers95,1212
Non-polymers764
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-44 kcal/mol
Surface area30800 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-23 kcal/mol
Surface area19760 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 area3570 Å2
ΔGint-23 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.420, 100.094, 170.226
Angle α, β, γ (deg.)90.00, 131.82, 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: unp residues 17-460 / Mutation: E148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: clcA, eriC, yadQ, b0155, JW5012 / 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)
#4: Chemical
ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: F
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: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG400, 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: 8.2.1 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→25 Å / Num. all: 71808 / Num. obs: 71781 / % possible obs: 99.8 % / 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: 2.85→25 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 34.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 3618 5.04 %random
Rwork0.2485 ---
obs0.2506 71781 99 %-
all-71808 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13215 0 4 0 13219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113543
X-RAY DIFFRACTIONf_angle_d1.01418426
X-RAY DIFFRACTIONf_dihedral_angle_d15.0474762
X-RAY DIFFRACTIONf_chiral_restr0.0632121
X-RAY DIFFRACTIONf_plane_restr0.0052312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7859-2.82250.4121920.38572049X-RAY DIFFRACTION79
2.8225-2.86120.38331410.35042657X-RAY DIFFRACTION100
2.8612-2.9020.3871490.33642598X-RAY DIFFRACTION100
2.902-2.94520.40861570.32182622X-RAY DIFFRACTION100
2.9452-2.99120.40841330.3312611X-RAY DIFFRACTION100
2.9912-3.04010.38851630.32332624X-RAY DIFFRACTION100
3.0401-3.09250.35261420.31072623X-RAY DIFFRACTION100
3.0925-3.14860.4051260.31562651X-RAY DIFFRACTION100
3.1486-3.2090.29671480.29752614X-RAY DIFFRACTION100
3.209-3.27440.3881470.30242628X-RAY DIFFRACTION100
3.2744-3.34540.40911200.30082649X-RAY DIFFRACTION100
3.3454-3.42310.33421440.3052622X-RAY DIFFRACTION100
3.4231-3.50840.34161300.29052677X-RAY DIFFRACTION100
3.5084-3.6030.29611460.27832622X-RAY DIFFRACTION100
3.603-3.70870.32371540.28532635X-RAY DIFFRACTION100
3.7087-3.8280.32481310.26952616X-RAY DIFFRACTION100
3.828-3.96430.30581490.26722647X-RAY DIFFRACTION100
3.9643-4.12240.29771110.25912680X-RAY DIFFRACTION100
4.1224-4.30910.28881280.24142655X-RAY DIFFRACTION100
4.3091-4.5350.2881530.22352643X-RAY DIFFRACTION100
4.535-4.81730.29191420.222640X-RAY DIFFRACTION100
4.8173-5.18620.2581280.21632679X-RAY DIFFRACTION100
5.1862-5.70250.24631490.22392649X-RAY DIFFRACTION100
5.7025-6.5150.3111420.23012682X-RAY DIFFRACTION100
6.515-8.16070.2341340.20522689X-RAY DIFFRACTION100
8.1607-25.0430.22411590.2162701X-RAY DIFFRACTION99

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