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- PDB-7vm8: Crystal structure of the MtDMI1 gating ring -

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Basic information

Entry
Database: PDB / ID: 7vm8
TitleCrystal structure of the MtDMI1 gating ring
ComponentsIon channel DMI1
KeywordsPLANT PROTEIN / DMI / symbiose
Function / homologyCASTOR/POLLUX/SYM8 ion channel, conserved domain / Ion channel CASTOR/POLLUX/SYM8-like / Castor and Pollux, part of voltage-gated ion channel / monoatomic ion transport / nuclear membrane / membrane => GO:0016020 / NAD(P)-binding domain superfamily / Ion channel DMI1
Function and homology information
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.034 Å
AuthorsHuang, X. / Zhang, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Constitutive activation of a nuclear-localized calcium channel complex in Medicago truncatula.
Authors: Liu, H. / Lin, J.S. / Luo, Z. / Sun, J. / Huang, X. / Yang, Y. / Xu, J. / Wang, Y.F. / Zhang, P. / Oldroyd, G.E.D. / Xie, F.
History
DepositionOct 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: Ion channel DMI1


Theoretical massNumber of molelcules
Total (without water)60,4751
Polymers60,4751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21900 Å2
Unit cell
Length a, b, c (Å)110.982, 110.982, 91.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Ion channel DMI1 / Does not make infections protein 1


Mass: 60475.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: DMI1 / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q6RHR6

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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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 16% (wt/vol) PEG 4000, 0.2M KCl, 0.01M CaCl2, 0.05 M Sodium cacodylate trihydrate pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 14703 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Χ2: 0.94 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.1112.30.97510870.8530.2890.90.606100
3.11-3.2311.70.61710670.9390.1880.6450.651100
3.23-3.3813.60.46910680.9660.1320.4880.714100
3.38-3.56140.33811040.9770.0940.3510.987100
3.56-3.7813.80.25810710.9820.0720.2681.112100
3.78-4.0713.50.19611010.990.0550.2031.463100
4.07-4.4812.80.10710720.9970.0310.1121.057100
4.48-5.1312.30.0810800.9970.0240.0831.061100
5.13-6.4613.90.06611030.9980.0180.0680.903100
6.46-1012.70.03911080.9990.0110.040.76999.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O6J

6o6j


Resolution: 3.034→45.8 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3193 733 4.99 %
Rwork0.2596 13970 -
obs0.2626 14703 69.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.14 Å2 / Biso mean: 47.0991 Å2 / Biso min: 14.64 Å2
Refinement stepCycle: final / Resolution: 3.034→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 0 0 3913
Num. residues----505
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0343-3.26850.3859770.3725151437
3.2685-3.59730.37741030.3511203751
3.5973-4.11760.36731320.2928251962
4.1176-5.18660.30532030.2334386997
5.1866-100.28562180.22324031100

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