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- PDB-2r9h: Crystal Structure of Q207C Mutant of CLC-ec1 in complex with Fab -

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Basic information

Entry
Database: PDB / ID: 2r9h
TitleCrystal Structure of Q207C Mutant of CLC-ec1 in complex with Fab
Components
  • (Fab fragmentFragment antigen-binding) x 2
  • H(+)/Cl(-) exchange transporter clcA
KeywordsMEMBRANE PROTEIN / CLC / antiporter / transporter / exchanger / disulfide / crosslink / Chloride / Inner membrane / Ion transport / Stress response / Transmembrane
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 / molecular replacement / Resolution: 3.1 Å
AuthorsNguitragool, W. / Miller, C.
CitationJournal: To be Published
Title: Crystal Structure of Q207C Mutant of CLC-ec1 in complex with Fab
Authors: Miller, C. / Nguitragool, W.
History
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 2, 2013Group: Source and taxonomy
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
D: Fab fragment
E: Fab fragment
F: Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,37310
Polymers188,2316
Non-polymers1424
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)233.099, 98.358, 171.922
Angle α, β, γ (deg.)90.000, 131.770, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: ALA / Refine code: 3 / Auth seq-ID: 18 - 458 / Label seq-ID: 2 - 442

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 47333.043 Da / Num. of mol.: 2 / Mutation: Q207C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clcA, eriC / Plasmid: pASK90 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P37019
#2: Antibody Fab fragment / Fragment antigen-binding


Mass: 23693.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Fab fragment / Fragment antigen-binding


Mass: 23088.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.5 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 9.5
Details: Vapor diffusion: 3 uL of protein complex, 7 mg/ml, in 50 mM NaKTartrate, 5 mM Tris, 12.5 mM NaCl, 18.5% w/v PEG300, 25 mM glycine against 300 uL of 25 mM NaCl, 37% w/v PEG300, 50 mM glycine, ...Details: Vapor diffusion: 3 uL of protein complex, 7 mg/ml, in 50 mM NaKTartrate, 5 mM Tris, 12.5 mM NaCl, 18.5% w/v PEG300, 25 mM glycine against 300 uL of 25 mM NaCl, 37% w/v PEG300, 50 mM glycine, pH 9.5, sitting drop, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9204 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9204 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 52974 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Χ2: 2.227 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.214.80.4850840.696196.7
3.21-3.3460.37153090.78199.6
3.34-3.496.70.28752720.932199.9
3.49-3.6870.21153041.168199.9
3.68-3.917.10.1653031.553199.9
3.91-4.217.20.12253542.255199.9
4.21-4.637.20.09253033.109199.8
4.63-5.370.07953723.565199.8
5.3-6.676.90.07153443.65199.7
6.67-506.50.04853293.734197.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.1 Å49.18 Å
Translation3.1 Å49.18 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.913 / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2638 5 %RANDOM
Rwork0.261 ---
obs0.262 52493 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 105.226 Å2
Baniso -1Baniso -2Baniso -3
1--3.29 Å20 Å2-0.8 Å2
2--3.2 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13217 0 4 0 13221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02213391
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.96218232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.65851725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17723.092469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.824152119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4031563
X-RAY DIFFRACTIONr_chiral_restr0.0630.22101
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029941
X-RAY DIFFRACTIONr_nbd_refined0.1920.26110
X-RAY DIFFRACTIONr_nbtor_refined0.3010.29277
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2345
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0340.22
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1732TIGHT POSITIONAL0.020.05
1496LOOSE POSITIONAL0.465
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 179 -
Rwork0.338 3584 -
all-3763 -
obs--97.08 %

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