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- PDB-2fec: Structure of the E203Q mutant of the Cl-/H+ exchanger CLC-ec1 fro... -

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Basic information

Entry
Database: PDB / ID: 2fec
TitleStructure of the E203Q mutant of the Cl-/H+ exchanger CLC-ec1 from E.Coli
Components
  • Fab fragment, heavy chainFragment antigen-binding
  • Fab fragment, light chainFragment antigen-binding
  • H(+)/Cl(-) exchange transporter clcA
KeywordsPROTON TRANSPORT / MEMBRANE PROTEIN / CLC-ec1 / CLCA_ECOLI / Chloride/Proton exchange transporter
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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.967 Å
AuthorsAccardi, A. / Walden, M.P. / Nguitragool, W. / Jayaram, H. / Williams, C. / Miller, C.
Citation
Journal: J.Gen.Physiol. / Year: 2005
Title: Separate ion pathways in a Cl-/H+ exchanger
Authors: Accardi, A. / Walden, M.P. / Nguitragool, W. / Jayaram, H. / Williams, C. / Miller, C.
#1: Journal: Science / Year: 2003
Title: Gating the selectivity filter in ClC chloride channels
Authors: Dutzler, R. / Cambell, E.B. / Mackinnon, R.
History
DepositionDec 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / 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
J: Fab fragment, heavy chain
O: Fab fragment, light chain
I: Fab fragment, heavy chain
L: Fab fragment, light chain


Theoretical massNumber of molelcules
Total (without water)193,1386
Polymers193,1386
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.311, 98.496, 170.415
Angle α, β, γ (deg.)90.00, 131.51, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: ALA / Refine code: 3 / Auth seq-ID: 18 - 458 / Label seq-ID: 18 - 458

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 49657.711 Da / Num. of mol.: 2 / Mutation: E203Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clcA, eriC / Plasmid: pASK-IBA2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37019
#2: Antibody Fab fragment, heavy chain / Fragment antigen-binding


Mass: 23823.031 Da / Num. of mol.: 2 / Fragment: Heavy Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 10EC3/G4 / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody Fab fragment, light chain / Fragment antigen-binding


Mass: 23088.443 Da / Num. of mol.: 2 / Fragment: Light Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 10EC3/G4 / Cell line (production host): hybridoma / 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: 3.73 Å3/Da / Density % sol: 67.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 250 mM NaBr, PEG 400 37%, 0.05 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9198 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 3.967→128.04 Å / Num. all: 25143 / Num. obs: 23320 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.967→128.04 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.866 / SU B: 59.536 / SU ML: 0.826 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.997 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32555 1258 5.1 %RANDOM
Rwork0.26892 ---
obs0.27184 23320 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 155.801 Å2
Baniso -1Baniso -2Baniso -3
1--5.61 Å20 Å2-0.43 Å2
2--5.41 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 3.967→128.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13223 0 0 0 13223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02213553
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.96218456
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09451743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35622.985479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76152145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8981567
X-RAY DIFFRACTIONr_chiral_restr0.070.22121
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210087
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.26819
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.29336
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2433
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4021.58874
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.724213912
X-RAY DIFFRACTIONr_scbond_it0.435440
X-RAY DIFFRACTIONr_scangle_it0.6854.54544
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1764tight positional0.040.05
1540loose positional0.45
1764tight thermal4.990.5
1540loose thermal4.7710
LS refinement shellResolution: 3.967→4.069 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 75 -
Rwork0.33 1461 -
obs--82.8 %

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