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- PDB-3ejz: Structure of E203V mutant E.coli Cl-/H+ exchanger, CLC-ec1 -

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Basic information

Entry
Database: PDB / ID: 3ejz
TitleStructure of E203V mutant E.coli Cl-/H+ exchanger, CLC-ec1
Components
  • Fab fragment, Heavy chain
  • Fab fragment, Light chain
  • H(+)/Cl(-) exchange transporter clcA
KeywordsIMMUNE SYSTEM/PROTON TRANSPORT / membrane protein / Cl-/H+ exchanger / Antiport / Cell inner membrane / Cell membrane / Chloride / Ion transport / Stress response / Transmembrane / Transport / IMMUNE SYSTEM-PROTON TRANSPORT 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 / B cell differentiation / extracellular region / 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / Immunoglobulin kappa constant / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLim, H.-H. / Miller, C.
CitationJournal: J.Gen.Physiol. / Year: 2009
Title: Intracellular proton-transfer mutants in a CLC Cl-/H+ exchanger.
Authors: Lim, H.H. / Miller, C.
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
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 / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
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)194,60510
Polymers194,2866
Non-polymers3204
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: H(+)/Cl(-) exchange transporter clcA
B: H(+)/Cl(-) exchange transporter clcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0406
Polymers100,7212
Non-polymers3204
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-49 kcal/mol
Surface area30750 Å2
MethodPISA
3
C: Fab fragment, Heavy chain
D: Fab fragment, Light chain


Theoretical massNumber of molelcules
Total (without water)46,7822
Polymers46,7822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-23 kcal/mol
Surface area19480 Å2
MethodPISA
4
E: Fab fragment, Heavy chain
F: Fab fragment, Light chain


Theoretical massNumber of molelcules
Total (without water)46,7822
Polymers46,7822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-23 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.259, 96.415, 170.150
Angle α, β, γ (deg.)90.00, 131.78, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

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


Mass: 50360.418 Da / Num. of mol.: 2 / Mutation: E203V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clcA, eriC, yadQ, b0155, JW5012 / 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: hybridoma
#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: hybridoma / References: UniProt: P01837*PLUS
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / 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: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 36% (w/v) PEG 300, 20 mM NaBr, 50 mM tris-SO4, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.9→60 Å / Num. all: 61705 / Num. obs: 58605 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 88.7 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 18.9
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / Num. unique all: 9005 / Rsym value: 0.54 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ots as a starting model

1ots


Resolution: 2.9→58.76 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 1.133 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28087 3094 5 %RANDOM
Rwork0.25191 ---
all0.253381 61705 --
obs0.25338 58605 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.464 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.5 Å2
2---0.02 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.9→58.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13219 0 4 0 13223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02213547
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.96218448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67251743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52422.956477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.193152143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7841567
X-RAY DIFFRACTIONr_chiral_restr0.0810.22123
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110071
X-RAY DIFFRACTIONr_mcbond_it8.4951.58655
X-RAY DIFFRACTIONr_mcangle_it11.769213910
X-RAY DIFFRACTIONr_scbond_it1.48634892
X-RAY DIFFRACTIONr_scangle_it2.5774.54538
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
1700medium positional0.030.5
1464loose positional0.035
1700medium thermal7.922
1464loose thermal8.0210
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 220 -
Rwork0.357 4325 -
obs-4325 99.63 %

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