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- PDB-5oxf: An oligomerised bacterial dynamin pair provides a mechanism for t... -

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Basic information

Entry
Database: PDB / ID: 5oxf
TitleAn oligomerised bacterial dynamin pair provides a mechanism for the long range sensing and tethering of membranes
Components(GTP-binding proteinG protein) x 2
KeywordsLIPID BINDING PROTEIN / dynamin / membrane remodelling / membrane fusion / membrane tethering.
Function / homology
Function and homology information


GTP binding / ATP binding
Similarity search - Function
Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ATP-binding protein / ATP-binding protein / Putative ATP/GTP binding protein / Putative ATP/GTP binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.94 Å
AuthorsLiu, J.W. / Noel, J.K. / Low, H.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust097328/Z/11/Z United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for membrane tethering by a bacterial dynamin-like pair.
Authors: Liu, J. / Noel, J.K. / Low, H.H.
History
DepositionSep 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein
B: GTP-binding protein
C: GTP-binding protein
D: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,1098
Polymers314,3364
Non-polymers1,7734
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14750 Å2
ΔGint-80 kcal/mol
Surface area133160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.717, 228.675, 318.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GTP-binding protein / G protein


Mass: 85217.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GDP / Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: BKM79_02020, CRM98_01430 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D9BJX7, UniProt: Q0PB99*PLUS
#2: Protein GTP-binding protein / G protein


Mass: 71951.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: BKM79_02025 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D9BKH6, UniProt: Q0PB98*PLUS
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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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: 6.65 Å3/Da / Density % sol: 81.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.7-1.0 M succinate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 3.94→185.8 Å / Num. obs: 74962 / % possible obs: 95.5 % / Redundancy: 3.8 % / Net I/σ(I): 14.6
Reflection shellResolution: 3.94→4.08 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.94→58.981 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 3491 4.88 %
Rwork0.2591 --
obs0.2604 71535 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.94→58.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19475 0 112 0 19587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419865
X-RAY DIFFRACTIONf_angle_d1.02926758
X-RAY DIFFRACTIONf_dihedral_angle_d18.2657298
X-RAY DIFFRACTIONf_chiral_restr0.0533083
X-RAY DIFFRACTIONf_plane_restr0.0053404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9401-3.99410.36451170.36922171X-RAY DIFFRACTION78
3.9941-4.05110.33671330.35882466X-RAY DIFFRACTION88
4.0511-4.11160.33951430.3592701X-RAY DIFFRACTION97
4.1116-4.17580.3181180.34992775X-RAY DIFFRACTION97
4.1758-4.24420.35311370.32462716X-RAY DIFFRACTION96
4.2442-4.31740.34011300.29712749X-RAY DIFFRACTION98
4.3174-4.39590.27281450.2842788X-RAY DIFFRACTION98
4.3959-4.48040.31551570.27052679X-RAY DIFFRACTION97
4.4804-4.57180.29331410.26082778X-RAY DIFFRACTION97
4.5718-4.67120.28981450.25752725X-RAY DIFFRACTION98
4.6712-4.77980.25971310.24512820X-RAY DIFFRACTION98
4.7798-4.89930.29651370.23462738X-RAY DIFFRACTION98
4.8993-5.03170.27191200.22152791X-RAY DIFFRACTION98
5.0317-5.17970.28491550.23332742X-RAY DIFFRACTION97
5.1797-5.34670.27361530.24092723X-RAY DIFFRACTION97
5.3467-5.53770.30481400.24432726X-RAY DIFFRACTION96
5.5377-5.75920.27861410.23982754X-RAY DIFFRACTION96
5.7592-6.02110.29531440.25842752X-RAY DIFFRACTION96
6.0211-6.33820.31451100.26992775X-RAY DIFFRACTION96
6.3382-6.73480.32711480.29342779X-RAY DIFFRACTION97
6.7348-7.25390.34531550.27592752X-RAY DIFFRACTION96
7.2539-7.98230.27631520.25322730X-RAY DIFFRACTION95
7.9823-9.13370.22451490.19892765X-RAY DIFFRACTION95
9.1337-11.49360.2121500.18422780X-RAY DIFFRACTION95
11.4936-58.9880.33941400.32472869X-RAY DIFFRACTION93

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