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- PDB-4kk6: Structure of CLC-ec1 deltaNC construct in 20mM Bromide -

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Basic information

Entry
Database: PDB / ID: 4kk6
TitleStructure of CLC-ec1 deltaNC construct in 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
BROMIDE 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: 3.183 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 20, 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)189,37910
Polymers189,0606
Non-polymers3204
Water00
1
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5566
Polymers95,2372
Non-polymers3204
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-45 kcal/mol
Surface area30410 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 area3680 Å2
ΔGint-23 kcal/mol
Surface area19640 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 area3660 Å2
ΔGint-22 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.362, 100.918, 171.718
Angle α, β, γ (deg.)90.00, 132.12, 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 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) / 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) / Production host: MUS MUSCULUS (house mouse)
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
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: 3.93 Å3/Da / Density % sol: 68.72 %
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: 8.2.2 / 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: 3.18→25 Å / Num. all: 95466 / Num. obs: 95417 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.093
Reflection shellResolution: 3.18→3.26 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 / Resolution: 3.183→24.882 Å / SU ML: 0.38 / σ(F): 1.95 / Phase error: 31.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 2462 5.05 %
Rwork0.2351 --
obs0.2369 95417 98.97 %
all-95466 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.183→24.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13214 0 4 0 13218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613542
X-RAY DIFFRACTIONf_angle_d0.76318424
X-RAY DIFFRACTIONf_dihedral_angle_d13.3594764
X-RAY DIFFRACTIONf_chiral_restr0.0472120
X-RAY DIFFRACTIONf_plane_restr0.0042312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1828-3.21890.38141050.34252207X-RAY DIFFRACTION72
3.2189-3.25670.39061620.34283039X-RAY DIFFRACTION99
3.2567-3.29640.41731500.3193011X-RAY DIFFRACTION100
3.2964-3.3380.31641550.3073090X-RAY DIFFRACTION100
3.338-3.38180.35571560.31033046X-RAY DIFFRACTION100
3.3818-3.4280.34431540.29713048X-RAY DIFFRACTION100
3.428-3.47690.32861670.29213049X-RAY DIFFRACTION100
3.4769-3.52860.34381750.27993050X-RAY DIFFRACTION100
3.5286-3.58360.29441440.26693104X-RAY DIFFRACTION100
3.5836-3.64220.29451340.26633013X-RAY DIFFRACTION100
3.6422-3.70480.30311640.2653110X-RAY DIFFRACTION100
3.7048-3.77190.27151640.26372979X-RAY DIFFRACTION100
3.7719-3.84420.33961840.25983070X-RAY DIFFRACTION100
3.8442-3.92240.25841480.25753082X-RAY DIFFRACTION100
3.9224-4.00730.2941580.25473057X-RAY DIFFRACTION100
4.0073-4.10020.34061360.26233016X-RAY DIFFRACTION100
4.1002-4.20220.25081920.22883105X-RAY DIFFRACTION100
4.2022-4.31530.25231580.23292998X-RAY DIFFRACTION100
4.3153-4.44160.28311490.21243042X-RAY DIFFRACTION100
4.4416-4.58410.29621740.22273070X-RAY DIFFRACTION100
4.5841-4.74680.25331860.22253025X-RAY DIFFRACTION100
4.7468-4.93550.24861530.20643022X-RAY DIFFRACTION100
4.9355-5.15820.31650.21633056X-RAY DIFFRACTION100
5.1582-5.42750.24821630.21153064X-RAY DIFFRACTION100
5.4275-5.76360.24851760.21843045X-RAY DIFFRACTION100
5.7636-6.20220.2511660.2213058X-RAY DIFFRACTION100
6.2022-6.81470.28251750.21223034X-RAY DIFFRACTION100
6.8147-7.77440.23561360.20023068X-RAY DIFFRACTION100
7.7744-9.69750.16181830.16863022X-RAY DIFFRACTION100
9.6975-24.88260.27181840.25913021X-RAY DIFFRACTION99

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