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- PDB-6lsc: Structure of the E202Y mutant of the Cl-/H+ antiporter CLC-ec1 fr... -

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Basic information

Entry
Database: PDB / ID: 6lsc
TitleStructure of the E202Y mutant of the Cl-/H+ antiporter CLC-ec1 from E.coli: a re-refined model of the 4FTP model
ComponentsH(+)/Cl(-) exchange transporter ClcA
KeywordsMEMBRANE PROTEIN / CLC chloride/proton antiporter
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsLim, H.H. / Shane, T. / Miller, C.
CitationJournal: PLoS Biol. / Year: 2012
Title: Intracellular proton access in a Cl(-)/H(+) antiporter.
Authors: Lim, H.H. / Shane, T. / Miller, C.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 26, 2020ID: 4FTP
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H(+)/Cl(-) exchange transporter ClcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7282
Polymers49,6931
Non-polymers351
Water181
1
A: H(+)/Cl(-) exchange transporter ClcA
hetero molecules

A: H(+)/Cl(-) exchange transporter ClcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4564
Polymers99,3862
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3940 Å2
ΔGint-61 kcal/mol
Surface area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.702, 85.166, 100.092
Angle α, β, γ (deg.)90.000, 102.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 49692.754 Da / Num. of mol.: 1 / Mutation: E202Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: clcA, eriC, yadQ, b0155, JW5012 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P37019
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.8 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 38% PEG400, 100mM CaCl2, 100mM Glycine-NaOH, pH 9.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2012
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: 3.2→25 Å / Num. obs: 12142 / % possible obs: 99 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 2
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.59 / Num. unique obs: 904 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OTS

1ots


Resolution: 3.21→24.43 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.879 / SU B: 18.55 / SU ML: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.451
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.263 637 5.2 %RANDOM
Rwork0.2101 ---
obs0.213 11500 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 239.86 Å2 / Biso mean: 96.111 Å2 / Biso min: 57.73 Å2
Baniso -1Baniso -2Baniso -3
1--3.93 Å2-0 Å23.78 Å2
2---6.85 Å20 Å2
3---8.26 Å2
Refinement stepCycle: final / Resolution: 3.21→24.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 1 1 3144
Biso mean--113.41 60.14 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133211
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173195
X-RAY DIFFRACTIONr_angle_refined_deg1.471.6184360
X-RAY DIFFRACTIONr_angle_other_deg1.191.5587327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5015420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3220.924119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.59515508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.821515
X-RAY DIFFRACTIONr_chiral_restr0.0620.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023569
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02696
LS refinement shellResolution: 3.213→3.296 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 36 -
Rwork0.293 868 -
all-904 -
obs--97.84 %

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