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- PDB-7cvs: Crystal structure of the C85A/L194A mutant CLC-ec1 with Fab fragment -

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Basic information

Entry
Database: PDB / ID: 7cvs
TitleCrystal structure of the C85A/L194A 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: 3.01 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)194,59710
Polymers194,4556
Non-polymers1424
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)232.909, 96.721, 170.731
Angle α, β, γ (deg.)90.000, 131.653, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 20 - 457 / Label seq-ID: 20 - 457

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and resid 20 through 458)AA
2(chain 'B' and resid 20 through 458)BB

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Components

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


Mass: 50316.258 Da / Num. of mol.: 2 / Mutation: C85A, L194A
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.: 4 / 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: 3.69 Å3/Da / Density % sol: 66.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 29% (w/v) PEG400 100 mM Hepes-NaOH (pH 7.0) 200 mM NaCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2017
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: 3.005→33.96 Å / Num. obs: 54754 / % possible obs: 96.45 % / Redundancy: 5.4 % / Biso Wilson estimate: 93.15 Å2 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.082 / Net I/σ(I): 24.1
Reflection shellResolution: 3.005→3.05 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.842 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 2148 / Rpim(I) all: 0.84 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ENE

4ene


Resolution: 3.01→33.96 Å / SU ML: 0.3992 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7803 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 2720 4.97 %random
Rwork0.2005 51974 --
obs0.2031 54694 96.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.45 Å2
Refinement stepCycle: LAST / Resolution: 3.01→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13235 0 4 0 13239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003913563
X-RAY DIFFRACTIONf_angle_d0.707318468
X-RAY DIFFRACTIONf_chiral_restr0.04412121
X-RAY DIFFRACTIONf_plane_restr0.00572318
X-RAY DIFFRACTIONf_dihedral_angle_d3.43927922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.060.4381310.36722171X-RAY DIFFRACTION78.19
3.06-3.120.39571540.32632771X-RAY DIFFRACTION98.19
3.12-3.180.321630.29682710X-RAY DIFFRACTION97.92
3.18-3.250.31281300.27342776X-RAY DIFFRACTION98.44
3.25-3.330.33391570.25792828X-RAY DIFFRACTION98.65
3.33-3.410.31581360.24172777X-RAY DIFFRACTION99.05
3.41-3.50.25431340.22062817X-RAY DIFFRACTION99.36
3.5-3.610.26741500.21612795X-RAY DIFFRACTION99.7
3.61-3.720.28021460.20932840X-RAY DIFFRACTION99.53
3.72-3.850.29081610.22767X-RAY DIFFRACTION99.9
3.85-4.010.26411360.19062862X-RAY DIFFRACTION99.8
4.01-4.190.24251390.1862814X-RAY DIFFRACTION99.66
4.19-4.410.23121230.16112819X-RAY DIFFRACTION98.82
4.41-4.690.21171720.15562761X-RAY DIFFRACTION98.36
4.69-5.050.18121330.15412814X-RAY DIFFRACTION98.07
5.05-5.550.24081530.16382767X-RAY DIFFRACTION98.45
5.55-6.350.22251550.18382835X-RAY DIFFRACTION99.2
6.35-7.990.19311330.20092788X-RAY DIFFRACTION96.37
7.99-33.960.31541140.22652262X-RAY DIFFRACTION76.94
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.00579607447921-0.07351157645360.07465335772881.268974630231.668433802881.566288260090.104976007143-0.596472967836-0.761702853270.1502342528810.0789971214281-0.252940077549-0.02888425083430.184592432889-0.0170671160040.671516501714-0.00903777662759-0.01651905365311.241417887470.1473946044820.928010929919278.6384605382.5120800312124.3011348097
20.7989978692460.8855713239351.199459971452.140172241061.777589794761.77357161487-0.300569637135-0.101695623104-0.0984019748291-0.513714427944-0.04909899621110.0181728652174-0.02428638780160.206704633975-0.07441139992260.9034454171640.2794225898690.001758966884150.9852273535670.005802727722571.1348809768276.298318972-8.061605191385.71355410466
31.33697551958-0.3334266972340.3966018874631.837541921470.5866828358591.52709904685-0.0701540144815-0.146472857498-0.428150760503-0.0499138201991-0.030526629659-0.03398548168640.4250792932670.9733666821440.0008692925878270.7281634259570.1996993910070.01183646486361.101233775020.1633660734150.903028417954279.796101063-3.7114727746826.381752631
40.981687542218-0.006552262049690.5838942571410.245251293746-0.6704854777210.6236103138820.204916714911-0.7670298180420.115348313888-0.581792169846-0.2186179055110.392147759810.175608008487-0.0192796629843-0.0001665771606881.024160998180.0860842073824-0.06965517957790.9357848814540.07370509340721.03530325996266.7164687569.1724923024822.7719699834
51.58822377747-0.960913441846-1.123010550791.162375426060.3501372241883.81953085666-0.1053853001280.0231427406983-0.551556809106-0.2172958406180.08142685415390.3678692192130.200391265068-0.1054101896430.0001419822038440.7414745337630.0830875041963-0.05836244944870.5901591875530.01024995529471.07646266143256.528182451-9.2798932777914.4994255916
60.702317161578-0.876746690672-0.3328436958170.5481815336980.7827274176041.149513087260.03524901449020.0592321159563-0.04842956172710.4104676582670.0730175918174-0.3466043314270.4055495277730.0771323721032-0.00047731608880.7607934377670.171391996711-0.02343179337630.8459150266540.1223266575741.26156968829264.7828634-15.707942764325.7119748831
71.62449608871-0.866565382847-0.4931863417222.21689024906-0.4115100106723.98175820269-0.581140522173-0.28352002379-0.7013935555591.22295707695-0.171541844380.549476929950.934171834069-0.553204764195-0.2627556501160.7506959758940.09440941783630.06532975750291.096795791580.4119450159071.0781639466257.111636688-7.0597889416446.2047341707
81.07720315080.9308405489750.9786149404271.469602028730.5960918552950.749825692701-0.0584446521192-0.771374556187-0.6285027481790.304970671075-0.1078488517580.01725264994080.0130894999717-0.08097917092640.1326511984521.18841989590.2817738718020.1180229662341.49599050920.514620984540.845739258267258.3705747624.4770505164164.1976361065
91.411664206150.1994789222410.3416852879790.680930158453-0.6116710450240.5946439174840.0924377406901-0.0827983395075-0.1118923960450.247719557696-0.0632088499505-0.475240067246-0.004415242915720.300033013680.0001201563984940.892565822340.212807490561-0.03336469649341.057290910250.3329453848661.03815972622263.402808803-8.5542274456148.1400968299
100.9182688631970.798244525882-0.4861999464220.815687408949-0.6208697125310.43220453275-0.0419840639010.0301932940376-0.322462349206-0.0576706018320.0517484865233-0.0393438607433-0.0862571442794-0.2557529828060.0003968567866921.001304936460.27111583140.01070032303961.224210410160.2271912658140.942708494616252.4678904443.5456720024138.9466395047
110.3186977154730.590552891176-0.8691758313870.519913732036-0.1839985774882.161985091050.0383916394471-0.304033982003-0.02024937449890.562190079616-0.03980368228980.0384357720968-1.10509348953-0.00924694326974-0.0002753051654111.283245633010.144525983041-0.07690538637711.406753870710.1272189787280.74158627914266.6378452217.811839750555.1891740573
121.16627153069-0.323223759828-0.2129192735770.042278893662-0.001864835971930.160680090223-0.215790256685-0.386857883588-0.05586315827270.3540882852190.13934563030.00901041504053-0.972054909863-0.2862731917040.0001262981940391.041639088960.0976201846924-0.08466319550680.9305209461670.04923900546640.65311966905266.4065008623.995728628338.2554254272
130.138510744491-0.9024462005330.02943769535892.54780738946-0.64481952340.801243712882-0.0250182820358-0.309238950221-0.003322813396140.0855175136425-0.386042340603-0.124644216481-0.4976020512440.529078113040.0005010303317940.935760381140.161184510117-0.05194995482711.252011795080.2390053320890.892068035488272.1066419997.7362475953443.9008718992
141.1765313214-1.33016229240.8934918727693.96382770499-0.9494418692862.92225876429-0.200268264550.0157809185298-0.42442267885-0.107614027345-0.0213308943445-0.055434335095-0.4266645785470.141466155926-0.0005783489328120.6953550963870.1707318561720.02564238118380.8502384910790.1223022453060.916906307829225.59176412414.844074780223.1383054606
152.14972869881-1.51712877240.9418422574581.71764790628-1.45566763630.9656733458630.03058946014910.216631014559-0.291161426922-0.346553916754-0.2230089532390.208443183678-0.003109848092430.219483976005-0.0004336588386650.6057341648870.168513363941-0.01669949181750.8722590804070.03412940848270.686574223048221.91344354913.912074469722.5448786241
160.8230053039530.287189975567-1.053209718361.35125625399-0.7138273323431.45400885888-0.65406230027-0.7283909497170.9822716600810.207258883978-0.383853837963-0.3061546128690.120202015307-0.439627591299-1.25094631190.8210183238720.1580074998560.07315898330581.65131165785-0.6598121006410.714712717657191.07844948938.421522093541.807134205
171.46966914437-1.09576848318-0.1688851239870.838426687288-0.18744111812.20952841213-0.365744253351-0.932976556071-0.06370613019970.4019738872470.01332488000410.0397134830384-0.2465411499590.4568163848270.0002899343062010.9093345525870.161736739878-0.03836126440051.25918161531-0.1961204034950.709280764357200.98850304135.394465823736.2972614632
181.0348872136-0.691722171291-0.08772039995530.598345316336-0.2887767058741.74448769326-0.021189511816-0.281493224948-0.3607954981720.7469364637810.3429218850450.8473981950690.409424553982-2.460354940630.09428759041150.9799508291570.3542387599470.1932085057481.259398989010.360801435091.17745673072214.6370764342.8245822645245.3536635115
191.50176602232-0.948156451776-0.5502949069310.577073947887-0.02231493788181.04106083677-0.344050502461-0.896457594511-0.4177841540880.512112156770.44387440203-0.624996565086-0.214576802787-0.1961931315160.0003792183669750.8179842374820.3217156999610.007395694309591.474955960730.2782513825831.01710743593225.0891115286.1625054274143.3544566401
201.27925394226-0.597840342973-0.6776349967620.8389385264060.4933387778510.208275921024-0.210053545993-0.612756747914-0.3735079552290.07102671631760.2994961080840.2146897472930.0113332223672-0.06857944558630.0003690811248690.8071908233550.3518760025390.07185882333251.507064687510.2423344479070.876105354755208.58850999916.430279081241.6096012024
210.892249223179-0.514575547255-0.4706110502462.40963082894-1.165602439730.9026278676220.237348656019-0.35002560154-0.490034868318-0.184366408140.176143247030.6170497325970.191957525441-0.14004636078-0.0004947742283510.7969774293150.2887042394990.03660359518391.445127164420.1612264080110.960455412932188.51393474524.063369389742.0983432144
223.658377986-2.2525268533-0.001510588415482.681452317850.1558260428771.82384512104-0.169423046687-0.01968665263090.08044095834250.3855916556160.0226795512542-0.0120402833137-0.115133114639-0.1766414842989.0316128884E-50.91729204468-0.07602612719770.06500441187750.4321195693730.006156684284430.61215215087254.5412784239.720695483218.2578287646
232.27317527536-0.805331697732-0.2041142486271.34517001899-0.6051902279471.56027727395-0.1245048245080.6770497626420.218231252183-0.2520945867930.2706794243180.0289246068667-0.06788824867530.160218130990.0002388676995530.867628329794-0.03697376421660.03234045337680.6470588165580.04627207767030.743442092786241.64312947647.2688487625-10.1596943626
240.945386933906-1.09631590826-0.5176061891671.58932965935-0.6378079418272.244044253-0.2031635356930.260451866971-0.1441355688750.1399120003930.0144043616405-0.228826991026-0.1042580508980.7565839869270.0005487712861410.821526035546-0.203896580342-0.03961813684020.6792425204710.06784467469870.72255562284270.66730808135.06429751173.03063440586
252.03577961656-1.23327897-0.2205481021411.846832761470.05036179609582.636546863280.2164149889580.6329181240370.258112890985-0.149690222319-0.402447574185-0.215119269882-0.590480531854-0.34457251336.63728970463E-50.990892453369-0.02620765077430.02483313907590.6317086503550.3115823908460.802251053164250.89300303556.3003778152-19.5795514226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 146 )
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 214 )
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 248 )
5X-RAY DIFFRACTION5chain 'A' and (resid 249 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 146 )
9X-RAY DIFFRACTION9chain 'B' and (resid 147 through 214 )
10X-RAY DIFFRACTION10chain 'B' and (resid 215 through 248 )
11X-RAY DIFFRACTION11chain 'B' and (resid 249 through 356 )
12X-RAY DIFFRACTION12chain 'B' and (resid 357 through 394 )
13X-RAY DIFFRACTION13chain 'B' and (resid 395 through 458 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 60 )
15X-RAY DIFFRACTION15chain 'C' and (resid 61 through 127 )
16X-RAY DIFFRACTION16chain 'C' and (resid 128 through 142 )
17X-RAY DIFFRACTION17chain 'C' and (resid 143 through 222 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 25 )
19X-RAY DIFFRACTION19chain 'D' and (resid 26 through 74 )
20X-RAY DIFFRACTION20chain 'D' and (resid 75 through 127 )
21X-RAY DIFFRACTION21chain 'D' and (resid 128 through 211 )
22X-RAY DIFFRACTION22chain 'E' and (resid 2 through 119 )
23X-RAY DIFFRACTION23chain 'E' and (resid 120 through 222 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 112 )
25X-RAY DIFFRACTION25chain 'F' and (resid 113 through 211 )

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