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Yorodumi- PDB-6k5d: Crystal structure of the E148N mutant CLC-ec1 in presence of 200 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k5d | |||||||||
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Title | Crystal structure of the E148N mutant CLC-ec1 in presence of 200 mM NaBr | |||||||||
Components |
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Keywords | MEMBRANE 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 | |||||||||
Biological species | Escherichia coli (E. coli) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.203 Å | |||||||||
Authors | Park, K. / Lim, H.H. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k5d.cif.gz | 336.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k5d.ent.gz | 272 KB | Display | PDB format |
PDBx/mmJSON format | 6k5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k5d_validation.pdf.gz | 484.3 KB | Display | wwPDB validaton report |
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Full document | 6k5d_full_validation.pdf.gz | 523.1 KB | Display | |
Data in XML | 6k5d_validation.xml.gz | 61.9 KB | Display | |
Data in CIF | 6k5d_validation.cif.gz | 84.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/6k5d ftp://data.pdbj.org/pub/pdb/validation_reports/k5/6k5d | HTTPS FTP |
-Related structure data
Related structure data | 6ad7C 6ad8C 6adaC 6adbC 6adcC 6k5aC 6k5fC 6k5iC 4eneS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50375.391 Da / Num. of mol.: 2 / Mutation: E148N 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 | 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: Mus musculus (house mouse) #3: Antibody | 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: Mus musculus (house mouse) #4: Chemical | ChemComp-BR / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 400 25% (V/V), 200 mM NaBr 100 mM Glycine |
-Data collection
Diffraction | Mean temperature: 77.36 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→42.9 Å / Num. obs: 92236 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.104 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4547 / CC1/2: 0.752 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ENE Resolution: 3.203→42.923 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.203→42.923 Å
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Refine LS restraints |
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LS refinement shell |
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