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- PDB-7cvt: Crystal structure of the C85A/L194A/H234C mutant CLC-ec1 with Fab... -

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Basic information

Entry
Database: PDB / ID: 7cvt
TitleCrystal structure of the C85A/L194A/H234C mutant CLC-ec1 with Fab fragment
Components
  • H(+)/Cl(-) exchange transporter ClcA
  • antibody Fab fragment heavy chain
  • antibody Fab fragment light chain
KeywordsTRANSPORT PROTEIN / CLC / Chloride / Dimer interface
Function / homologyChloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / voltage-gated chloride channel activity / antiporter activity / chloride transmembrane transporter activity / plasma membrane => GO:0005886 / H(+)/Cl(-) exchange transporter ClcA
Function and homology information
Biological speciesEscherichia coli MS 198-1 (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPark, K. / Mersch, K. / Robertson, J. / Lim, H.-H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future Planning (MSIP)20-BR-01-05 Korea, Republic Of
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Altering CLC stoichiometry by reducing non-polar side-chains at the dimerization interface.
Authors: Mersch, K. / Ozturk, T.N. / Park, K. / Lim, H.H. / Robertson, J.L.
History
DepositionAug 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: antibody Fab fragment heavy chain
D: antibody Fab fragment light chain
E: antibody Fab fragment heavy chain
F: antibody Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,4929
Polymers194,3856
Non-polymers1063
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)233.034, 98.305, 172.434
Angle α, β, γ (deg.)90.00, 131.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 50281.254 Da / Num. of mol.: 2 / Mutation: C85A, L194A, H234C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli MS 198-1 (bacteria) / Gene: clcA, eriC, HMPREF9552_04837 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D7XDR7
#2: Antibody antibody Fab fragment 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 antibody Fab fragment 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)
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
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: 3.78 Å3/Da / Density % sol: 67.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 25% (w/v) PEG 400 100mM Glycine, pH 9.5 100mM Li2NO3

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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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2018
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 63778 / % possible obs: 98.9 % / Redundancy: 5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.126 / Net I/σ(I): 36.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.7 % / Rmerge(I) obs: 2.064 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 3059 / CC1/2: 0.516 / % possible all: 96

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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
Resolution: 2.9→50 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 3294 5.17 %random
Rwork0.2006 ---
obs0.2026 63725 98.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13245 0 3 0 13248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613571
X-RAY DIFFRACTIONf_angle_d0.96518478
X-RAY DIFFRACTIONf_dihedral_angle_d6.2077932
X-RAY DIFFRACTIONf_chiral_restr0.052123
X-RAY DIFFRACTIONf_plane_restr0.0062320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.94990.35671780.31922881X-RAY DIFFRACTION96
2.9499-3.00350.33211640.31473046X-RAY DIFFRACTION100
3.0035-3.06130.33541570.27573042X-RAY DIFFRACTION100
3.0613-3.12370.2971550.26563036X-RAY DIFFRACTION100
3.1237-3.19160.30961910.25213019X-RAY DIFFRACTION100
3.1916-3.26580.29761690.26143018X-RAY DIFFRACTION100
3.2658-3.34740.30971610.25273036X-RAY DIFFRACTION100
3.3474-3.43780.31531420.24863058X-RAY DIFFRACTION100
3.4378-3.53880.28322040.22643001X-RAY DIFFRACTION100
3.5388-3.65290.31921900.21953005X-RAY DIFFRACTION100
3.6529-3.78340.24351600.20833062X-RAY DIFFRACTION100
3.7834-3.93460.28271200.19673099X-RAY DIFFRACTION100
3.9346-4.11340.25631790.19013016X-RAY DIFFRACTION100
4.1134-4.32990.20771730.17373048X-RAY DIFFRACTION100
4.3299-4.60060.20951600.15943057X-RAY DIFFRACTION100
4.6006-4.95480.20641610.16333077X-RAY DIFFRACTION100
4.9548-5.45170.21121640.16883049X-RAY DIFFRACTION100
5.4517-6.23640.24061600.19683098X-RAY DIFFRACTION100
6.2364-7.84170.2281580.19743076X-RAY DIFFRACTION100
7.8417-500.19771480.20642707X-RAY DIFFRACTION85
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.60960.2013-0.39841.98111.02312.9484-0.1856-0.295-0.531-0.2896-0.0365-0.15490.33160.38790.21510.71520.30290.08181.0468-0.06730.9819161.5539-4.3403142.1202
21.6164-0.1775-0.04052.3469-0.08012.6892-0.1893-1.1609-1.31360.19380.0708-0.15460.58710.76630.08750.78440.3190.06011.22460.17441.0216164.1314-4.5405154.8143
36.33380.5816-0.03570.38920.21030.0331-0.0466-0.1569-0.14970.15110.08960.2897-0.1902-0.2880.0060.98280.27490.02181.0659-0.00530.9788151.32658.5203151.3329
41.48280.7998-0.29460.6686-1.21393.00560.01720.4729-1.1275-0.5853-0.08620.70220.3125-0.1990.01520.95620.1727-0.01750.5987-0.02261.0432143.6401-12.7664139.5123
50.35550.7764-0.84811.9879-0.89612.6439-0.04970.0693-0.5578-0.17280.0290.25440.0913-0.20150.01440.62560.2711-0.01410.7468-0.00021.0111138.1513-6.8457146.6638
62.5147-1.0527-0.16081.93460.50251.8044-0.7077-0.5246-0.58350.25970.75340.0440.63640.420.01210.77470.25330.08530.87110.10471.205148.9853-16.2817154.2691
72.6386-0.5681-1.44571.6341-0.53533.6629-0.1327-0.8533-0.29460.21770.48060.128-0.03520.0244-0.21730.82640.20380.01711.12540.34791.0464141.6371-7.533174.7242
81.80760.0326-0.02522.78850.80892.2012-0.0217-1.5388-0.98531.35630.4089-0.2551-0.47620.06990.83251.82670.70470.33131.86350.59450.3568144.04455.7834193.5475
90.79540.22130.83661.3476-0.70862.3513-0.6037-1.3204-0.82630.72370.6585-0.20640.50970.44610.01061.13890.54890.15021.43720.48681.0459146.1312-6.5484180.1164
100.87721.4356-0.06383.7066-1.68521.3073-0.0661-0.31450.17090.18920.08240.4062-0.3294-0.0531-0.09461.0320.35750.06091.15140.25430.8866137.1733.2857167.5236
11-0.05120.1379-0.2871.803-0.62613.5439-0.3175-0.69520.05450.79980.1151-0.1155-0.7845-0.32070.14381.1490.4196-0.15071.29240.01940.6712153.176615.259177.0116
124.7778-0.84360.23652.9352-0.6630.9679-0.40530.08080.6042-0.4754-0.266-0.0568-0.6066-0.04480.67710.9520.1565-0.1110.877-0.11191.0019104.117121.6649150.4232
132.4485-1.43531.16064.2262-1.16313.7633-0.421-0.4948-0.45950.17350.0291-0.0617-0.12410.62710.26480.6010.2313-0.01370.9060.07570.8879112.102312.3293152.2041
149.39411.88631.60254.3974-0.92228.3926-0.01751.4202-1.1923-0.912-0.59950.2630.4291.31040.5360.81270.38010.02451.1987-0.07230.9123108.22588.4822143.8938
157.3485-1.8551-0.20131.8655-0.82734.14790.23080.7247-1.1686-0.2904-0.5782-0.3242-0.00120.88730.27280.83350.2982-0.10711.2254-0.00930.7574105.667415.5406145.442
164.3856-2.2235-0.14041.7887-0.8421.4827-0.3258-0.5448-0.4389-0.05170.09820.25110.00210.11170.31220.66270.2004-0.06980.80970.04240.8302106.239614.7467156.4923
172.6103-0.31751.70091.665-0.97883.7743-0.7017-0.40890.60340.5121-0.54640.76190.2355-1.04880.08710.87410.36280.08661.3896-0.65960.954175.529138.3523169.8576
181.6654-0.7096-1.30760.54090.05022.6918-0.619-1.750.20660.90140.1701-0.4752-0.07280.95790.5720.99750.3838-0.05821.5983-0.24610.800387.274932.6216165.1978
190.73351.7061.35255.17294.36976.7198-0.6646-1.6527-0.13860.56961.0021.0672-0.0455-0.60520.60220.83890.46970.06841.1714-0.19530.621882.932228.227162.3322
202.12260.4299-3.58152.5192-0.19756.1291-0.2982-1.3540.63061.0149-0.64250.2693-1.0577-0.27260.22851.1440.3463-0.25591.7723-0.52510.788486.395141.2681166.8813
216.5945-2.7504-5.85683.97792.659.72-0.23590.14431.48610.52660.2023-0.0681-0.3772-0.08090.16270.98430.1309-0.1271.0643-0.30941.049282.27342.4948161.8684
222.5514-0.7527-0.76073.7081.58842.1618-0.2425-1.3922-0.93731.4097-0.11570.39730.0803-2.50560.32650.96020.47690.18591.7290.62241.326699.14363.0755174.1551
231.98150.306-0.11593.5162-0.40553.8006-0.4327-1.3676-1.20250.91430.4016-0.4073-0.07660.19380.14490.8620.54870.06381.68130.38141.2033109.59136.2549172.0143
241.8533-0.5976-1.31610.55230.93551.5238-0.5012-1.5186-0.83420.26740.28220.566-0.0699-0.58070.11351.02060.55640.03711.810.32951.1154100.55619.4583172.3212
251.4756-0.20460.85323.1841-0.30842.8735-0.3395-0.7192-0.37660.01290.40930.49540.3064-0.228-0.13290.9120.49870.04191.55980.11180.959673.003325.84169.5446
263.401-0.61780.37488.3215-1.16251.9999-0.2606-0.22710.6549-0.2606-0.14880.2424-0.6865-0.30860.51931.126-0.08560.07850.8373-0.11411.1296132.04244.6417141.8975
273.6951.9211-0.70632.25712.16175.6071-0.01970.3631-0.99270.7935-0.51970.7114-0.1536-1.09860.51951.04490.03060.08660.6258-0.10310.915135.164531.1057147.5029
284.5655-1.0967-0.41283.8093-0.38934.0792-0.4482-0.56920.58840.75710.1985-0.0093-0.694-0.04750.19740.93270.0291-0.01250.4808-0.03380.6872140.243440.4055149.8943
292.2612-0.01950.33590.322-0.93411.9669-0.08540.03660.3302-0.2309-0.01720.1322-0.0895-0.08650.08961.0189-0.0561-0.09220.5731-0.00850.8145138.652242.6886139.1722
304.265-1.7271-0.65465.85990.06220.11660.1561.01860.1304-1.04940.1716-0.1403-0.83260.4394-0.0240.80570.0417-0.06530.90010.150.8635127.236247.3138109.2286
313.87610.1642-0.63914.262-0.01684.5209-0.37980.65850.49340.57350.4724-0.60470.03630.1240.05260.7498-0.0016-0.07780.59990.07050.7863131.104746.3347120.739
323.0762-0.3615-0.01613.62392.16657.76580.00760.4641-0.40090.04860.01810.85430.9848-1.4103-0.270.9092-0.1416-0.0920.88890.05580.9993121.026943.1979116.1525
331.87660.1822-0.47911.7472-0.54764.2655-0.34620.26340.07550.33560.0658-0.3238-0.08810.69670.21380.8107-0.1418-0.17680.69410.06660.8098156.801833.0503132.7688
342.5351-0.88740.47411.4449-0.80182.6914-0.54950.34780.09750.15050.3701-0.7269-0.50040.78890.27270.9618-0.2172-0.10580.63850.03770.7329153.890535.7112134.382
351.3213-0.78150.56721.5497-0.5421.1818-0.0676-0.14660.331-0.49330.29960.2822-0.4415-0.3046-0.09791.0551-0.1078-0.1370.92530.22690.938136.229649.1865111.5857
362.8336-1.9170.15683.61960.50440.80420.21660.62791.04090.2345-0.0337-0.4907-1.1080.74530.08651.0434-0.22180.2230.630.59291.2685139.992553.466109.1553
373.8378-0.89390.20413.886-1.1113.3786-0.3554-0.02190.3770.45050.4967-0.3299-0.9666-0.558-0.14451.1047-0.2453-0.07351.05720.26990.8423141.514752.3135113.1441
382.729-0.29760.0613.2764-0.58974.92990.59051.16851.9881-1.7456-0.6992-0.1623-2.5021-1.2399-0.00771.90130.1302-0.2570.91070.38521.322130.711262.6543108.0024
392.1234-0.33341.23671.8881-0.792.07890.37721.06180.5945-0.4523-0.5913-0.6639-1.57730.15250.27641.22290.1940.07571.42430.33860.8973138.417654.3024100.4013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 146 )
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 214 )
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 248 )
4X-RAY DIFFRACTION4chain 'A' and (resid 249 through 329 )
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 418 )
6X-RAY DIFFRACTION6chain 'A' and (resid 419 through 460 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 70 )
8X-RAY DIFFRACTION8chain 'B' and (resid 71 through 123 )
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 214 )
10X-RAY DIFFRACTION10chain 'B' and (resid 215 through 248 )
11X-RAY DIFFRACTION11chain 'B' and (resid 249 through 458 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 17 )
13X-RAY DIFFRACTION13chain 'C' and (resid 18 through 60 )
14X-RAY DIFFRACTION14chain 'C' and (resid 61 through 73 )
15X-RAY DIFFRACTION15chain 'C' and (resid 74 through 91 )
16X-RAY DIFFRACTION16chain 'C' and (resid 92 through 127 )
17X-RAY DIFFRACTION17chain 'C' and (resid 128 through 142 )
18X-RAY DIFFRACTION18chain 'C' and (resid 143 through 176 )
19X-RAY DIFFRACTION19chain 'C' and (resid 177 through 192 )
20X-RAY DIFFRACTION20chain 'C' and (resid 193 through 210 )
21X-RAY DIFFRACTION21chain 'C' and (resid 211 through 222 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 25 )
23X-RAY DIFFRACTION23chain 'D' and (resid 26 through 74 )
24X-RAY DIFFRACTION24chain 'D' and (resid 75 through 112 )
25X-RAY DIFFRACTION25chain 'D' and (resid 113 through 211 )
26X-RAY DIFFRACTION26chain 'E' and (resid 2 through 17 )
27X-RAY DIFFRACTION27chain 'E' and (resid 18 through 33 )
28X-RAY DIFFRACTION28chain 'E' and (resid 34 through 83 )
29X-RAY DIFFRACTION29chain 'E' and (resid 84 through 132 )
30X-RAY DIFFRACTION30chain 'E' and (resid 133 through 153 )
31X-RAY DIFFRACTION31chain 'E' and (resid 154 through 192 )
32X-RAY DIFFRACTION32chain 'E' and (resid 193 through 222 )
33X-RAY DIFFRACTION33chain 'F' and (resid 1 through 74 )
34X-RAY DIFFRACTION34chain 'F' and (resid 75 through 101 )
35X-RAY DIFFRACTION35chain 'F' and (resid 102 through 127 )
36X-RAY DIFFRACTION36chain 'F' and (resid 128 through 149 )
37X-RAY DIFFRACTION37chain 'F' and (resid 150 through 173 )
38X-RAY DIFFRACTION38chain 'F' and (resid 174 through 196 )
39X-RAY DIFFRACTION39chain 'F' and (resid 197 through 211 )

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