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- PDB-2htk: Structure of the Escherichia coli ClC chloride channel Y445A muta... -

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Basic information

Entry
Database: PDB / ID: 2htk
TitleStructure of the Escherichia coli ClC chloride channel Y445A mutant and Fab complex
Components
  • Fab fragment, Heavy chain
  • Fab fragment, Light chain
  • H(+)/Cl(-) exchange transporter clcA
KeywordsMEMBRANE PROTEIN / ClC family of channel and transporters / H+/Cl- antiporter / Fab complex
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 / : / 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 / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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
BROMIDE ION / H(+)/Cl(-) exchange transporter ClcA / Ighg protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å
AuthorsAccardi, A. / Lobet, S. / Williams, C. / Miller, C. / Dutzler, R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Synergism between halide binding and proton transport in a CLC-type exchanger
Authors: Accardi, A. / Lobet, S. / Williams, C. / Miller, C. / Dutzler, R.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 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 / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 fragment, Heavy chain
D: Fab fragment, Light chain
E: Fab fragment, Heavy chain
F: Fab fragment, Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,3218
Polymers194,1616
Non-polymers1602
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)232.067, 98.139, 171.068
Angle α, β, γ (deg.)90.00, 131.56, 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 auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 5 / 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 / 1ECCLC H+/CL- ANTIPORTER / CLC-EC1


Mass: 50298.309 Da / Num. of mol.: 2 / Mutation: Y445A mutation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clcA, eriC / Plasmid: pet 28b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P37019
#2: Antibody Fab fragment, Heavy chain


Mass: 23693.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA CELL LINE / References: UniProt: Q4VBH1*PLUS
#3: Antibody Fab fragment, Light chain


Mass: 23088.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA CELL LINE
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / 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: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 41% peg 300 w/v, 50mM Tris, 150mM NaKTart, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9193 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 14, 2006
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9193 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. all: 37458 / Num. obs: 36035 / % possible obs: 97.04 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 78.155 Å2 / Rmerge(I) obs: 0.073
Reflection shellResolution: 3.2→3.28 Å / % possible all: 75.14

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OTS

1ots


Resolution: 3.41→40 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / ESU R: 0.594 / ESU R Free: 0.586 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27609 1933 5.1 %RANDOM
Rwork0.26577 ---
all0.2663 ---
obs0.2663 36035 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.054 Å2
Baniso -1Baniso -2Baniso -3
1--6.27 Å20 Å2-0.99 Å2
2--6.71 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 3.41→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13209 0 2 0 13211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02213535
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9581.96218430
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.56751743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05822.998477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.974152143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0471567
X-RAY DIFFRACTIONr_chiral_restr0.060.22121
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210063
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.26528
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.29390
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2422
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.216
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0260.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it17.8141.58655
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it24.302213906
X-RAY DIFFRACTIONr_scbond_it0.76234880
X-RAY DIFFRACTIONr_scangle_it1.1664.54524
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
1764medium positional0.160.5
1533loose positional0.385
1764medium thermal11.532
1533loose thermal14.4910
LS refinement shellResolution: 3.41→3.502 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 139 -
Rwork0.354 2525 -
obs--92.69 %

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