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- PDB-4lou: Structure of the E148Q mutant of CLC-ec1 deltaNC construct in the... -

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Basic information

Entry
Database: PDB / ID: 4lou
TitleStructure of the E148Q mutant of CLC-ec1 deltaNC construct in the absence of halide
Components
  • Fab heavy chain
  • Fab light chain
  • H(+)/Cl(-) exchange transporter ClcA
Keywordsmembrane protein / tranport protein / Cl-/H+ antiporter
Function / homology
Function and homology information


chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / chloride transmembrane transport / proton 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: 2.981 Å
AuthorsLim, H.-H. / Miller, C.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: A fluoride interloper in a CLC-type Cl /H+ antiporter
Authors: Lim, H.-H. / Stockbridge, R.B. / Miller, C.
History
DepositionJul 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)189,0586
Polymers189,0586
Non-polymers00
Water00
1
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA


Theoretical massNumber of molelcules
Total (without water)95,2352
Polymers95,2352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-42 kcal/mol
Surface area31140 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 area3660 Å2
ΔGint-23 kcal/mol
Surface area19960 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 area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.617, 100.316, 170.955
Angle α, β, γ (deg.)90.00, 131.71, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer.

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Components

#1: Protein H(+)/Cl(-) exchange transporter ClcA / ClC-ec1


Mass: 47617.418 Da / Num. of mol.: 2 / Fragment: CLC-ec1 deltaNC / Mutation: E148Q
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)

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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: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 23% PEG 400, 20mM 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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2013
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: 2.98→40 Å / Num. obs: 55897 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 26.1
Reflection shellResolution: 2.98→3.05 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.426 / % possible all: 91.6

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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
Starting model: pdb entry 4ENE

4ene


Resolution: 2.981→39.724 Å / SU ML: 0.41 / σ(F): 1.38 / Phase error: 30.19 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 2976 5.06 %random
Rwork0.21 ---
obs0.2122 55897 98.28 %-
all-58842 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.981→39.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13243 0 0 0 13243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113571
X-RAY DIFFRACTIONf_angle_d1.26818462
X-RAY DIFFRACTIONf_dihedral_angle_d15.5794778
X-RAY DIFFRACTIONf_chiral_restr0.0812123
X-RAY DIFFRACTIONf_plane_restr0.0062318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9815-3.03030.3527980.31741865X-RAY DIFFRACTION70
3.0303-3.08260.38031470.29142580X-RAY DIFFRACTION96
3.0826-3.13860.3691330.29222684X-RAY DIFFRACTION99
3.1386-3.19890.36591460.26632663X-RAY DIFFRACTION100
3.1989-3.26420.37681400.25832701X-RAY DIFFRACTION100
3.2642-3.33510.36851350.24022741X-RAY DIFFRACTION100
3.3351-3.41270.27091380.23352682X-RAY DIFFRACTION100
3.4127-3.4980.29621300.23382682X-RAY DIFFRACTION100
3.498-3.59250.31191630.21862688X-RAY DIFFRACTION100
3.5925-3.69810.30511180.22462736X-RAY DIFFRACTION100
3.6981-3.81740.26031600.21542685X-RAY DIFFRACTION100
3.8174-3.95370.25921180.21272699X-RAY DIFFRACTION100
3.9537-4.11190.26321420.20982698X-RAY DIFFRACTION100
4.1119-4.29880.2551280.19042726X-RAY DIFFRACTION100
4.2988-4.52510.22681530.17792690X-RAY DIFFRACTION100
4.5251-4.80820.23751740.1752673X-RAY DIFFRACTION100
4.8082-5.17870.21071500.17512696X-RAY DIFFRACTION100
5.1787-5.69850.23311550.17692734X-RAY DIFFRACTION100
5.6985-6.520.241500.19622724X-RAY DIFFRACTION100
6.52-8.20260.2051340.18982749X-RAY DIFFRACTION100
8.2026-39.72740.21621640.23492770X-RAY DIFFRACTION99

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