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- PDB-7adi: KirBac3.1 W46R: role of a highly conserved tryptophan at the memb... -

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Basic information

Entry
Database: PDB / ID: 7adi
TitleKirBac3.1 W46R: role of a highly conserved tryptophan at the membrane-water interface of Kir channel
ComponentsInward rectifier potassium channel Kirbac3.1
KeywordsMEMBRANE PROTEIN / Metal transport / ion channel / inward rectifier / potassium channel
Function / homology
Function and homology information


inward rectifier potassium channel activity / monoatomic ion channel complex / identical protein binding
Similarity search - Function
Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Potassium channel domain / Ion channel / Immunoglobulin E-set
Similarity search - Domain/homology
: / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVenien-Bryan, C. / Fagnen, C. / De Zorzi, R. / Bannwarth, L. / Oubella, I. / Haouz, A.
Funding support France, Finland, 3items
OrganizationGrant numberCountry
Other private19928 France
Other governmentANR-EQUIPEX France
Other governmentMRT Finland
CitationJournal: Int J Mol Sci / Year: 2021
Title: Integrative Study of the Structural and Dynamical Properties of a KirBac3.1 Mutant: Functional Implication of a Highly Conserved Tryptophan in the Transmembrane Domain.
Authors: Fagnen, C. / Bannwarth, L. / Oubella, I. / Zuniga, D. / Haouz, A. / Forest, E. / Scala, R. / Bendahhou, S. / De Zorzi, R. / Perahia, D. / Venien-Bryan, C.
History
DepositionSep 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Inward rectifier potassium channel Kirbac3.1
B: Inward rectifier potassium channel Kirbac3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6496
Polymers67,5082
Non-polymers1424
Water41423
1
A: Inward rectifier potassium channel Kirbac3.1
B: Inward rectifier potassium channel Kirbac3.1
hetero molecules

A: Inward rectifier potassium channel Kirbac3.1
B: Inward rectifier potassium channel Kirbac3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,29812
Polymers135,0154
Non-polymers2838
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area18710 Å2
ΔGint-127 kcal/mol
Surface area50640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.770, 113.980, 89.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1001-

K

21A-1002-

K

31A-1003-

K

41A-1004-

MG

51B-413-

HOH

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Components

#1: Protein Inward rectifier potassium channel Kirbac3.1


Mass: 33753.750 Da / Num. of mol.: 2 / Mutation: W46R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magnetotacticum (bacteria)
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D9N164
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.02 Å3/Da / Density % sol: 69.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 15% (w/v) PEG- MME 5k, 15% (v/v) glycerol, 1M Lithium Chloride, and 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07114 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07114 Å / Relative weight: 1
ReflectionResolution: 2.8→48.34 Å / Num. obs: 189833 / % possible obs: 99.6 % / Redundancy: 7.1 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rsym value: 0.0558 / Net I/σ(I): 19.67
Reflection shellResolution: 2.83→3 Å / Rmerge(I) obs: 1.551 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 29583 / CC1/2: 0.659 / Rsym value: 1.44 / % possible all: 98.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0266refinement
BUSTERrefinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XL6

1xl6


Resolution: 2.8→48.02 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.825 / SU B: 13.663 / SU ML: 0.26 / SU R Cruickshank DPI: 0.441 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.441 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2873 1372 5 %RANDOM
Rwork0.2218 ---
obs0.225 26051 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 216.78 Å2 / Biso mean: 97.464 Å2 / Biso min: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0 Å2
2---1.09 Å20 Å2
3---0.86 Å2
Refinement stepCycle: final / Resolution: 2.8→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4246 0 4 23 4273
Biso mean--83.28 79.24 -
Num. residues----541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134386
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174087
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.635960
X-RAY DIFFRACTIONr_angle_other_deg1.2061.5659351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3455541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67920.171234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.38215687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.931535
X-RAY DIFFRACTIONr_chiral_restr0.0640.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024975
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021074
LS refinement shellResolution: 2.8→2.871 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.346 96 -
Rwork0.341 1814 -
obs--96.81 %

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