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- PDB-5hd8: Crystal structure of disulfide cross-linked D417C ClC-ec1 -

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Basic information

Entry
Database: PDB / ID: 5hd8
TitleCrystal structure of disulfide cross-linked D417C ClC-ec1
Components
  • FAB FRAGMENT (HEAVY CHAIN)
  • FAB FRAGMENT (LIGHT CHAIN)
  • H(+)/Cl(-) exchange transporter ClcA
KeywordsTRANSPORT PROTEIN / antiporter / membrane exchanger
Function / homology
Function and homology information


chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel 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
H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsMathews, I.I. / Khantwal, C.M. / Maduke, M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1021472 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM087519 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM086749 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41-RR05969 United States
CitationJournal: To be published
Title: Conformational change in CLC transporters: beyond the rotation of Gluex
Authors: Khantwal, C.M. / Abraham, S.J. / Han, W. / Jiang, T. / Chavan, T.S. / Cheng, R.C. / Elvington, S.M. / Liu, C.W. / Mathews, I.I. / Stein, R.A. / Mchaourab, H.S. / Tajkhorshid, E. / Maduke, M.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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)190,03510
Polymers189,8936
Non-polymers1424
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17530 Å2
ΔGint-154 kcal/mol
Surface area66480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.740, 96.060, 169.950
Angle α, β, γ (deg.)90.00, 131.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 48034.969 Da / Num. of mol.: 2 / Mutation: D417C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: clcA, eriC, yadQ, b0155, JW5012 / Plasmid: pASK-IBA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37019
#2: 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) / Cell line (production host): ST10C3/G4 / Production host: Mus musculus (house mouse)
#3: 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) / Cell line (production host): ST10C3/G4 / 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 9
Details: 30% PEG 400, 0.075M K/Na-tartrate, 0.1M Tris.HCl (pH 9.0)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: used cryostream
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2014
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.15→39.2 Å / Num. obs: 44041 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.76
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.74 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OTS

1ots


Resolution: 3.15→39.2 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.874 / SU B: 45.257 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25732 2202 5 %RANDOM
Rwork0.20537 ---
obs0.20793 41839 90.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 105.994 Å2
Baniso -1Baniso -2Baniso -3
1--4.31 Å20 Å2-0.72 Å2
2--13.72 Å20 Å2
3----3.41 Å2
Refinement stepCycle: 1 / Resolution: 3.15→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13064 0 4 0 13068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01913390
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212889
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.96118229
X-RAY DIFFRACTIONr_angle_other_deg0.7413.00129590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06851720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24622.872470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.912152118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4721567
X-RAY DIFFRACTIONr_chiral_restr0.0610.22094
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023048
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 142 -
Rwork0.324 2710 -
obs--80.79 %
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)
10.8927-0.6970.14880.8950.01611.3176-0.0273-0.0231-0.4519-0.1524-0.02840.11460.04050.26830.05570.45850.1715-0.04260.11560.03050.540735.3147-20.731317.99
20.7549-0.0510.05460.58170.04711.4854-0.0984-0.356-0.28260.24850.08720.0142-0.22740.0770.01120.60540.2385-0.02360.31950.1980.222230.396-9.14750.0382
32.6361-1.2976-0.32191.14290.1110.1195-0.0359-0.3507-0.21110.0268-0.0666-0.0738-0.0950.06840.10260.45290.1436-0.0970.29170.0360.3228-19.36187.941628.4295
42.9758-1.0764-0.25881.52250.09050.1972-0.2808-0.7412-0.60410.19560.24680.1847-0.0641-0.03830.0340.3890.2919-0.01390.46950.20080.2837-28.22440.625542.6288
51.4215-0.5486-0.0410.6821-0.29371.1109-0.15610.03430.17010.28790.02590.0905-0.2087-0.06640.13010.67990.0029-0.0260.00640.01540.439915.834528.23165.6455
61.4337-0.71310.43920.6976-0.5561.9521-0.01450.26520.23180.1681-0.0574-0.1258-0.35450.19520.07190.6627-0.1317-0.0570.14490.14350.426828.048530.1717-8.109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 458
2X-RAY DIFFRACTION2B18 - 458
3X-RAY DIFFRACTION3C2 - 222
4X-RAY DIFFRACTION4D1 - 211
5X-RAY DIFFRACTION5E2 - 221
6X-RAY DIFFRACTION6F1 - 211

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