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- PDB-6k5f: Crystal structure of the CLC-ec1 deltaNC in presence of 200 mM NaBr -

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Basic information

Entry
Database: PDB / ID: 6k5f
TitleCrystal structure of the CLC-ec1 deltaNC in presence of 200 mM NaBr
Components
  • Fab fragment, heavy chainFragment antigen-binding
  • Fab fragment, light chainFragment antigen-binding
  • H(+)/Cl(-) exchange transporter ClcA
KeywordsMEMBRANE PROTEIN / Cl- / H+ antiporter / CLC transporter
Function / homology
Function and homology information


chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / antiporter 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / H(+)/Cl(-) exchange transporter ClcA / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.203 Å
AuthorsPark, K. / Lim, H.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future Planning19-BR-01-02 Korea, Republic Of
Ministry of Science, ICT and Future Planning2017M3C7A 1048086 Korea, Republic Of
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Mutation of external glutamate residue reveals a new intermediate transport state and anion binding site in a CLC Cl-/H+antiporter.
Authors: Park, K. / Lee, B.C. / Lim, H.H.
History
DepositionMay 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2019Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 22, 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

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)194,92310
Polymers194,6046
Non-polymers3204
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)230.789, 101.656, 172.003
Angle α, β, γ (deg.)90.00, 132.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 50390.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Escherichia coli (E. coli)
Gene: yadQ, clcA, eriC, A6592_03060, A9819_00720, A9R57_04335, AC067_04570, AC789_1c01550, ACN002_0160, ACN81_28610, ACU57_18640, AM270_18100, AM446_22830, AMK83_01920, AWP75_13405, B1K96_13065, ...Gene: yadQ, clcA, eriC, A6592_03060, A9819_00720, A9R57_04335, AC067_04570, AC789_1c01550, ACN002_0160, ACN81_28610, ACU57_18640, AM270_18100, AM446_22830, AMK83_01920, AWP75_13405, B1K96_13065, B7C53_01430, B9M99_16180, BANRA_02286, BANRA_02303, BANRA_03326, BB545_20825, BE963_14760, BER14_07860, BFD29_18565, BHF46_07945, BHS81_00575, BHS87_00725, BIQ87_00715, BIU72_13480, BJJ90_21425, BK292_13605, BK373_09530, BK383_20300, BMT53_09575, BMT91_01430, BN17_45791, BVL39_02260, BXT93_20950, BZL31_15015, BZL69_20275, C2M16_10720, C2U48_09685, C3444_11105, C3449_15895, C4J69_03510, C5715_17420, C5P01_08850, C5P43_19885, C7235_20305, C7B02_09235, CG691_14570, CIJ94_20900, COD46_06560, CR538_20715, CRD98_15250, CRM83_15165, CRT46_00820, CV83915_01419, CWM24_04960, CWS33_09545, CXB56_23210, D2184_08665, D2185_20055, D2188_12715, D3821_06135, D3822_17405, D3I61_01530, D3O91_03110, D3Y67_10980, D5618_10265, D5653_16505, D8K42_10345, D9D20_18555, D9D29_16860, D9D31_08820, D9D55_03155, D9D69_06945, D9E22_13175, D9E34_01170, D9F17_00235, D9F57_04830, D9H66_18270, D9H68_13700, D9H94_13970, D9I47_04165, D9I87_01705, D9I88_06500, D9I97_03880, D9J03_00240, D9J11_16750, D9J44_14145, D9J60_02140, DL545_20465, DLW18_08025, DMZ31_06935, DNQ26_06330, DP277_13800, DQF57_05740, DQO13_06325, DS732_05700, DTL43_06000, DTM10_02705, DTM45_12560, DU321_03585, EAI42_18265, EAI44_17040, EAI46_14565, EAI52_10940, EC1094V2_3697, EC3234A_2c01370, Eco118UI_00790, EEP23_00240, EFV01_09785, EFV02_20350, EFV04_15100, EFV08_17265, EFV11_08020, EFV12_18730, EFV14_08750, EFV15_17340, EFV17_09990, EIA10_05995, EL75_3609, EL79_3718, EL80_3665, EOL26_04835, ERS085366_02706, ERS085379_00551, ERS150873_01097, GJ11_00825, HMPREF3040_02596, MJ49_06260, NCTC10082_01396, NCTC10090_02173, NCTC10429_04214, NCTC11126_03619, NCTC12950_04437, NCTC13148_05172, NCTC7922_05796, NCTC7927_04520, NCTC8009_07339, NCTC8179_01364, NCTC8500_04562, NCTC8959_04830, NCTC9036_04037, NCTC9037_04203, NCTC9044_03171, NCTC9050_02039, NCTC9055_00980, NCTC9058_02783, NCTC9062_04200, NCTC9073_03413, NCTC9077_05114, NCTC9111_04278, NCTC9702_04777, NCTC9703_03448, NCTC9706_01351, NCTC9777_00485, PU06_23100, RG28_03970, RK56_028075, RX35_04890, SAMEA3472044_04171, SAMEA3472055_02614, SAMEA3472070_02408, SAMEA3472090_04472, SAMEA3472110_04526, SAMEA3472112_04666, SAMEA3472147_00367, SAMEA3484427_01361, SAMEA3484429_01120, SAMEA3484433_03082, SAMEA3485113_00827, SAMEA3752372_04445, SAMEA3752553_02908, SAMEA3752557_00860, SAMEA3752559_03726, SAMEA3752620_02075, SAMEA3753097_03891, SAMEA3753164_02448, SK85_00155, UC41_07360, UN86_07645, WQ89_09495, WR15_02265, YDC107_3382
Production host: Escherichia coli (E. coli) / References: UniProt: J7Q633, UniProt: P37019*PLUS
#2: Antibody Fab fragment, heavy chain / Fragment antigen-binding


Mass: 23823.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab fragment, light chain / Fragment antigen-binding


Mass: 23088.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br

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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: 3.85 Å3/Da / Density % sol: 68.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 400 25% (v/v), 200mM NaBr 100 mM Tris-SO4

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Data collection

DiffractionMean temperature: 77.36 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.2→44.7 Å / Num. obs: 93832 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.973 / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.2
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 4720 / CC1/2: 0.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ENE

4ene


Resolution: 3.203→44.7 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 33.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2998 4680 5 %
Rwork0.2356 --
obs0.2387 93665 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.203→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13243 0 4 0 13247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213571
X-RAY DIFFRACTIONf_angle_d1.37618478
X-RAY DIFFRACTIONf_dihedral_angle_d4.3217928
X-RAY DIFFRACTIONf_chiral_restr0.0622123
X-RAY DIFFRACTIONf_plane_restr0.0082318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.203-3.23940.3797840.35741596X-RAY DIFFRACTION53
3.2394-3.27750.40151520.3443020X-RAY DIFFRACTION100
3.2775-3.31750.40131660.31363016X-RAY DIFFRACTION100
3.3175-3.35950.3641800.30662984X-RAY DIFFRACTION100
3.3595-3.40370.37851410.29273029X-RAY DIFFRACTION100
3.4037-3.45030.35291560.28143022X-RAY DIFFRACTION100
3.4503-3.49950.31741420.28263091X-RAY DIFFRACTION100
3.4995-3.55170.34321480.28012982X-RAY DIFFRACTION100
3.5517-3.60720.28751600.2643005X-RAY DIFFRACTION100
3.6072-3.66630.32121880.27142939X-RAY DIFFRACTION100
3.6663-3.72950.31291960.27593019X-RAY DIFFRACTION100
3.7295-3.79730.39441960.26652998X-RAY DIFFRACTION100
3.7973-3.87030.34251520.28722965X-RAY DIFFRACTION100
3.8703-3.94930.35331500.27323074X-RAY DIFFRACTION100
3.9493-4.03510.32141500.27033032X-RAY DIFFRACTION100
4.0351-4.12890.34041200.26253036X-RAY DIFFRACTION100
4.1289-4.23210.29971840.24933011X-RAY DIFFRACTION100
4.2321-4.34640.30241600.23713050X-RAY DIFFRACTION100
4.3464-4.47420.31231700.23232976X-RAY DIFFRACTION100
4.4742-4.61840.31941800.22473040X-RAY DIFFRACTION100
4.6184-4.78330.26681480.21972979X-RAY DIFFRACTION100
4.7833-4.97460.26661420.20223047X-RAY DIFFRACTION100
4.9746-5.20070.28331480.21283015X-RAY DIFFRACTION100
5.2007-5.47440.25111660.20333082X-RAY DIFFRACTION100
5.4744-5.81680.29131610.21082979X-RAY DIFFRACTION100
5.8168-6.26480.32981440.21893010X-RAY DIFFRACTION100
6.2648-6.89320.24031760.21073024X-RAY DIFFRACTION100
6.8932-7.88590.24851660.19752995X-RAY DIFFRACTION100
7.8859-9.91760.2341450.17383026X-RAY DIFFRACTION100
9.9176-44.76830.31891090.24832943X-RAY DIFFRACTION96

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