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- PDB-4kk8: Structure of the E148Q mutant of CLC-ec1 deltaNC construct in 100... -

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Basic information

Entry
Database: PDB / ID: 4kk8
TitleStructure of the E148Q mutant of CLC-ec1 deltaNC construct in 100mM fluoride
Components
  • Fab, heavy chain
  • Fab, light chain
  • H(+)/Cl(-) exchange transporter ClcA
KeywordsTRANSPORT PROTEIN / membrane transporter
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
FLUORIDE 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: 2.86 Å
AuthorsLim, H.-H. / Miller, C.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Fluoride-dependent interruption of the transport cycle of a CLC Cl(-)/H(+) antiporter.
Authors: Lim, H.H. / Stockbridge, R.B. / Miller, C.
History
DepositionMay 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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, heavy chain
D: Fab, light chain
E: Fab, heavy chain
F: Fab, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,0968
Polymers189,0586
Non-polymers382
Water00
1
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2734
Polymers95,2352
Non-polymers382
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-47 kcal/mol
Surface area30750 Å2
MethodPISA
2
C: Fab, heavy chain
D: Fab, light chain


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-23 kcal/mol
Surface area19640 Å2
MethodPISA
3
E: Fab, heavy chain
F: Fab, light chain


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-23 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.226, 98.903, 170.022
Angle α, β, γ (deg.)90.00, 131.77, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 25:455 )
211chain 'B' and (resseq 25:455 )
112chain 'D' and (resseq 1:7 or resseq 13:25 or resseq...
212chain 'F' and (resseq 1:7 or resseq 13:25 or resseq...
113chain 'D' and (resseq 37:39 or resseq 81:84 or resseq...
213chain 'F' and (resseq 37:39 or resseq 81:84 or resseq...
114chain 'D' and (resseq 8:12 or resseq 26:28 or resseq 40:45 or resseq 52:59 or resseq 66:68 )
214chain 'F' and (resseq 8:12 or resseq 26:28 or resseq 40:45 or resseq 52:59 or resseq 66:68 )
115chain 'C' and (resseq 2:123 or resseq 154:156 or resseq 174:178 or resseq 181:183 )
215chain 'E' and (resseq 2:123 or resseq 154:156 or resseq 174:178 or resseq 181:183 )
116chain 'C' and (resseq 124:153 or resseq 157:173 or resseq 184:222 )
216chain 'E' and (resseq 124:153 or resseq 157:173 or resseq 184:222 )

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 47617.418 Da / Num. of mol.: 2 / Fragment: unp residues 17-460 / Mutation: E148Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0155, clcA, eriC, JW5012, yadQ / Production host: Escherichia coli (E. coli) / References: UniProt: P37019
#2: Antibody Fab, heavy chain


Mass: 23823.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: MUS MUSCULUS (house mouse)
#3: Antibody Fab, light chain


Mass: 23088.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: MUS MUSCULUS (house mouse) / References: UniProt: P01837*PLUS
#4: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
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: 3.83 Å3/Da / Density % sol: 67.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG400, 100mM Na/K tartrate, 100mM Glycine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
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: 2.86→25 Å / Num. all: 65741 / Num. obs: 65721 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→24.95 Å / SU ML: 0.38 / σ(F): 1.95 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 3326 5.06 %
Rwork0.2099 --
obs0.2122 65721 98.96 %
all-65741 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.86→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13225 0 2 0 13227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913553
X-RAY DIFFRACTIONf_angle_d1.22718438
X-RAY DIFFRACTIONf_dihedral_angle_d15.1944770
X-RAY DIFFRACTIONf_chiral_restr0.0762121
X-RAY DIFFRACTIONf_plane_restr0.0062314
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3214X-RAY DIFFRACTIONPOSITIONAL
12B3214X-RAY DIFFRACTIONPOSITIONAL0.249
21D1031X-RAY DIFFRACTIONPOSITIONAL
22F1031X-RAY DIFFRACTIONPOSITIONAL1.417
31D332X-RAY DIFFRACTIONPOSITIONAL
32F332X-RAY DIFFRACTIONPOSITIONAL0.73
41D168X-RAY DIFFRACTIONPOSITIONAL
42F168X-RAY DIFFRACTIONPOSITIONAL0.265
51C1054X-RAY DIFFRACTIONPOSITIONAL
52E1054X-RAY DIFFRACTIONPOSITIONAL0.688
61C604X-RAY DIFFRACTIONPOSITIONAL
62E604X-RAY DIFFRACTIONPOSITIONAL0.312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8571-2.89780.33741150.30712167X-RAY DIFFRACTION82
2.8978-2.9410.351280.28062421X-RAY DIFFRACTION94
2.941-2.98690.29981460.27772630X-RAY DIFFRACTION99
2.9869-3.03580.34191410.26692574X-RAY DIFFRACTION100
3.0358-3.0880.30931270.26662645X-RAY DIFFRACTION100
3.088-3.14410.34521570.25982584X-RAY DIFFRACTION100
3.1441-3.20440.32541200.24892635X-RAY DIFFRACTION100
3.2044-3.26970.32881460.24522593X-RAY DIFFRACTION100
3.2697-3.34060.3151400.23712613X-RAY DIFFRACTION100
3.3406-3.41820.29281360.2432653X-RAY DIFFRACTION100
3.4182-3.50340.31741660.23262574X-RAY DIFFRACTION100
3.5034-3.59790.25531440.22232597X-RAY DIFFRACTION100
3.5979-3.70340.28241400.22092640X-RAY DIFFRACTION100
3.7034-3.82250.26631440.21212590X-RAY DIFFRACTION100
3.8225-3.95860.2511380.20612647X-RAY DIFFRACTION100
3.9586-4.11650.24381390.20482613X-RAY DIFFRACTION100
4.1165-4.30290.20971330.18722628X-RAY DIFFRACTION100
4.3029-4.52850.23461540.17852624X-RAY DIFFRACTION100
4.5285-4.81030.21131280.17662632X-RAY DIFFRACTION100
4.8103-5.17870.22581350.17712647X-RAY DIFFRACTION100
5.1787-5.69420.26231250.1842663X-RAY DIFFRACTION100
5.6942-6.50540.24771490.19782642X-RAY DIFFRACTION100
6.5054-8.14850.20011150.19362693X-RAY DIFFRACTION100
8.1485-24.95130.24661600.22472690X-RAY DIFFRACTION99

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