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- PDB-5yh0: The structure of DrFam20C1 -

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Basic information

Entry
Database: PDB / ID: 5yh0
TitleThe structure of DrFam20C1
ComponentsDrFam20C1
KeywordsTRANSFERASE / kinase
Function / homologyFAM20, C-terminal / FAM20 / Golgi casein kinase, C-terminal, Fam20 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Golgi apparatus / ATP binding / metal ion binding / membrane / FAM20C golgi-associated secretory pathway kinase a
Function and homology information
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.45 Å
AuthorsZhang, H. / Xiao, J.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Nat Commun / Year: 2018
Title: Structure and evolution of the Fam20 kinases
Authors: Zhang, H. / Zhu, Q. / Cui, J. / Wang, Y. / Chen, M.J. / Guo, X. / Tagliabracci, V.S. / Dixon, J.E. / Xiao, J.
History
DepositionSep 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: DrFam20C1
B: DrFam20C1
C: DrFam20C1
D: DrFam20C1
E: DrFam20C1
F: DrFam20C1
G: DrFam20C1
H: DrFam20C1
I: DrFam20C1
J: DrFam20C1
K: DrFam20C1
L: DrFam20C1


Theoretical massNumber of molelcules
Total (without water)774,06412
Polymers774,06412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20190 Å2
ΔGint-43 kcal/mol
Surface area194810 Å2
Unit cell
Length a, b, c (Å)114.925, 135.988, 219.971
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DrFam20C1


Mass: 64505.363 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: E7FBB8*PLUS
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Ammonium citrate tribasic pH 7.0, 0.1 M Imidazole pH 7.0, 18% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. obs: 88916 / % possible obs: 99.5 % / Redundancy: 3.7 % / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.45→47.843 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.11
RfactorNum. reflection% reflection
Rfree0.2785 2003 2.26 %
Rwork0.2247 --
obs0.2259 88731 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.45→47.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37919 0 0 0 37919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00438896
X-RAY DIFFRACTIONf_angle_d1.00352570
X-RAY DIFFRACTIONf_dihedral_angle_d15.85423683
X-RAY DIFFRACTIONf_chiral_restr0.0535613
X-RAY DIFFRACTIONf_plane_restr0.0066784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.53630.36451400.30596026X-RAY DIFFRACTION97
3.5363-3.63190.33931430.28856196X-RAY DIFFRACTION99
3.6319-3.73870.31661460.26726144X-RAY DIFFRACTION99
3.7387-3.85930.30281400.24586187X-RAY DIFFRACTION99
3.8593-3.99720.34721440.24336163X-RAY DIFFRACTION99
3.9972-4.15710.28991400.22576149X-RAY DIFFRACTION99
4.1571-4.34620.28121470.21486159X-RAY DIFFRACTION99
4.3462-4.57520.28121400.20836213X-RAY DIFFRACTION100
4.5752-4.86160.29081420.19336210X-RAY DIFFRACTION100
4.8616-5.23650.23641430.19296262X-RAY DIFFRACTION100
5.2365-5.76270.27171420.21596213X-RAY DIFFRACTION100
5.7627-6.59470.26371460.22216224X-RAY DIFFRACTION100
6.5947-8.30160.26581440.21786241X-RAY DIFFRACTION99
8.3016-47.84720.21111460.19716341X-RAY DIFFRACTION99

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