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- PDB-6v2j: Crystal structure of ClC-ec1 triple mutant (E113Q, E148Q, E203Q) -

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Basic information

Entry
Database: PDB / ID: 6v2j
TitleCrystal structure of ClC-ec1 triple mutant (E113Q, E148Q, E203Q)
ComponentsH(+)/Cl(-) exchange transporter ClcA
KeywordsTRANSPORT PROTEIN / chloride transporters / CLC-ec1
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 / 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 / molecular replacement / Resolution: 2.62 Å
AuthorsMaduke, M. / Mathews, I.I. / Chavan, T.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)41GM103393) United States
American Heart Association17POST33670553 United States
CitationJournal: Elife / Year: 2020
Title: A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the CLC Cl - /H + transport cycle.
Authors: Chavan, T.S. / Cheng, R.C. / Jiang, T. / Mathews, I.I. / Stein, R.A. / Koehl, A. / Mchaourab, H.S. / Tajkhorshid, E. / Maduke, M.
History
DepositionNov 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)52,2194
Polymers52,1121
Non-polymers1063
Water99155
1
A: H(+)/Cl(-) exchange transporter ClcA
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)104,4388
Polymers104,2252
Non-polymers2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area4610 Å2
ΔGint-109 kcal/mol
Surface area32170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.970, 120.440, 122.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 52112.402 Da / Num. of mol.: 1 / Mutation: E113Q, E148Q, E203Q
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) / Strain (production host): K12 / References: UniProt: P37019
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 289 K / Method: lipidic cubic phase / pH: 8.5
Details: 100mM Tris, 100mM sodium malonate, 30% PEG 400, 2.5% 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.62→28.65 Å / Num. obs: 17991 / % possible obs: 97.5 % / Redundancy: 7.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.086 / Rrim(I) all: 0.185 / Net I/σ(I): 8.4
Reflection shellResolution: 2.62→2.73 Å / Rmerge(I) obs: 0.866 / Num. unique obs: 1830 / CC1/2: 0.831 / Rrim(I) all: 1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOLREPphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OTS

1ots


Resolution: 2.62→28.65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2534 / WRfactor Rwork: 0.1844 / FOM work R set: 0.756 / SU B: 31.132 / SU ML: 0.294 / SU R Cruickshank DPI: 0.2717 / SU Rfree: 0.3105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 962 5.3 %RANDOM
Rwork0.1928 ---
obs0.1964 17029 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.27 Å2 / Biso mean: 60.26 Å2 / Biso min: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.54 Å2-0 Å2-0 Å2
2---0.28 Å2-0 Å2
3----5.26 Å2
Refinement stepCycle: final / Resolution: 2.62→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3241 0 3 55 3299
Biso mean--83.95 70.2 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133325
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173300
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.624517
X-RAY DIFFRACTIONr_angle_other_deg1.3061.5587574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.545436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08520.698129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42215533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4051518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
X-RAY DIFFRACTIONr_rigid_bond_restr2.07433325
LS refinement shellResolution: 2.62→2.683 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.293 69 -
Rwork0.282 968 -
obs--77.91 %
Refinement TLS params.Method: refined / Origin x: 35.5522 Å / Origin y: 28.1049 Å / Origin z: -18.3937 Å
111213212223313233
T0.0005 Å20.0009 Å2-0.006 Å2-0.1695 Å20.0023 Å2--0.1894 Å2
L0.2404 °20.0235 °2-0.1223 °2-0.241 °20.085 °2--0.5498 °2
S-0.008 Å °0.0257 Å °0.0208 Å °0.0042 Å °0.0052 Å °0.002 Å °0.0044 Å °-0.0126 Å °0.0027 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 63
2X-RAY DIFFRACTION1A64 - 73
3X-RAY DIFFRACTION1A74 - 158
4X-RAY DIFFRACTION1A159 - 233
5X-RAY DIFFRACTION1A234 - 266
6X-RAY DIFFRACTION1A267 - 386
7X-RAY DIFFRACTION1A387 - 454
8X-RAY DIFFRACTION1A455 - 464

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