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- PDB-2h2s: Crystal Structure of E148A mutant of CLC-ec1 in SeCN- -

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Basic information

Entry
Database: PDB / ID: 2h2s
TitleCrystal Structure of E148A mutant of CLC-ec1 in SeCN-
Components
  • CLC Cl transporter
  • FAB fragment, heavy chain
  • FAB fragment, light chain
KeywordsION TRANSPORT / CLC / transporter / chloride / antiport
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 / : / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
SELENOCYANATE 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: 3.1 Å
AuthorsNguitragool, W. / Miller, C.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Uncoupling of a CLC Cl(-)/H(+) Exchange Transporter by Polyatomic Anions
Authors: Nguitragool, W. / Miller, C.
History
DepositionMay 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 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 1.4Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLC Cl transporter
B: CLC Cl transporter
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)193,39612
Polymers192,7666
Non-polymers6306
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.927, 118.688, 148.915
Angle α, β, γ (deg.)90.000, 127.440, 90.000
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: 3 / Auth seq-ID: 18 - 454 / Label seq-ID: 18 - 454

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe complex is a homodimer of chains A and B along with nonequivalent Fab fragments

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Components

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


Mass: 49600.660 Da / Num. of mol.: 2 / Mutation: E148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clcA, eriC / Production host: Escherichia coli (E. coli) / 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-SEK / SELENOCYANATE ION


Mass: 104.977 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNSe
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: 3.95 Å3/Da / Density % sol: 68.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM KSeCN, 100 mM NaKTartrate, 38% PEG 300, 50 mM HEPES, 10 mM Tris.H2SO4, pH 7.5, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98 Å
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.034→169.031 Å / Num. obs: 54172 / % possible obs: 99.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.273.20.3462.12539178870.34699.8
3.27-3.473.20.2293.12406774820.22999.8
3.47-3.713.20.1524.62257370200.15299.6
3.71-43.20.1046.22098365420.10499.7
4-4.383.20.0757.91930060370.07599.6
4.38-4.93.20.0619.91738454570.06199.6
4.9-5.663.10.05610.81519648380.05699.6
5.66-6.933.10.05211.41253140530.05298.9
6.93-9.82.90.03715.8920131200.03798.1
9.8-117.8530.04311.1513417360.04396.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.1 Å48.86 Å
Translation3.1 Å48.86 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.943 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2714 5 %RANDOM
Rwork0.281 ---
all0.2811 ---
obs0.2811 54118 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.99 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å2-2.9 Å2
2--5.77 Å20 Å2
3----6.89 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13215 0 6 0 13221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213545
X-RAY DIFFRACTIONr_angle_refined_deg1.531.96218446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.49851743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76222.956477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.518152141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1091567
X-RAY DIFFRACTIONr_chiral_restr0.1050.22121
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210079
X-RAY DIFFRACTIONr_nbd_refined0.3410.28463
X-RAY DIFFRACTIONr_nbtor_refined0.3450.29583
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2692
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3640.22
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
1748TIGHT POSITIONAL0.050.05
1520LOOSE POSITIONAL0.295
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 186 -
Rwork0.392 3812 -
obs-3998 99.85 %

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