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- PDB-5yh3: The structure of hFam20C and hFam20A complex -

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Basic information

Entry
Database: PDB / ID: 5yh3
TitleThe structure of hFam20C and hFam20A complex
Components
  • Extracellular serine/threonine protein kinase FAM20C
  • Pseudokinase FAM20A
KeywordsTRANSFERASE / complex / kinase
Function / homology
Function and homology information


osteoclast maturation / regulation of phosphorus metabolic process / tooth eruption / regulation of fibroblast growth factor receptor signaling pathway / protein metabolic process => GO:0019538 / dentinogenesis / biomineral tissue development / phosphotransferase activity, alcohol group as acceptor / odontoblast differentiation / enamel mineralization ...osteoclast maturation / regulation of phosphorus metabolic process / tooth eruption / regulation of fibroblast growth factor receptor signaling pathway / protein metabolic process => GO:0019538 / dentinogenesis / biomineral tissue development / phosphotransferase activity, alcohol group as acceptor / odontoblast differentiation / enamel mineralization / calcium ion homeostasis / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / ATP metabolic process / protein serine/threonine kinase activator activity / post-translational protein modification / Post-translational protein phosphorylation / response to bacterium / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / manganese ion binding / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / protein phosphorylation / protein serine/threonine kinase activity / calcium ion binding / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / ATP binding / cytoplasm
Similarity search - Function
FAM20, C-terminal / FAM20 / Golgi casein kinase, C-terminal, Fam20
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Extracellular serine/threonine protein kinase FAM20C / Pseudokinase FAM20A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZhu, Q. / Xiao, J.
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 25, 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: Pseudokinase FAM20A
C: Extracellular serine/threonine protein kinase FAM20C
B: Pseudokinase FAM20A
D: Extracellular serine/threonine protein kinase FAM20C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,3248
Polymers208,2954
Non-polymers2,0294
Water00
1
A: Pseudokinase FAM20A
C: Extracellular serine/threonine protein kinase FAM20C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1624
Polymers104,1482
Non-polymers1,0142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-9 kcal/mol
Surface area36400 Å2
MethodPISA
2
B: Pseudokinase FAM20A
D: Extracellular serine/threonine protein kinase FAM20C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1624
Polymers104,1482
Non-polymers1,0142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-9 kcal/mol
Surface area36140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.469, 192.747, 226.669
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 Pseudokinase FAM20A


Mass: 53464.199 Da / Num. of mol.: 2 / Fragment: UNP residues 63-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM20A, UNQ9388/PRO34279 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96MK3
#2: Protein Extracellular serine/threonine protein kinase FAM20C / Dentin matrix protein 4 / DMP-4 / Golgi casein kinase / Golgi-enriched fraction casein kinase / GEF-CK


Mass: 50683.367 Da / Num. of mol.: 2 / Fragment: UNP residues 141-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM20C, DMP4 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8IXL6, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O13P3 / Comment: ATP, 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: 4.11 Å3/Da / Density % sol: 70.11 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1M BICINE pH 9.0, 2%(v/v) 1,4-Dioxane, 7%(w/v) Polyethylene glycol 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 75772 / % possible obs: 99.7 % / Redundancy: 5 % / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→48.557 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.74
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2658 3463 4.57 %
Rwork0.2328 --
obs0.2343 75772 75.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→48.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12888 0 124 0 13012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413356
X-RAY DIFFRACTIONf_angle_d0.71918097
X-RAY DIFFRACTIONf_dihedral_angle_d15.0498115
X-RAY DIFFRACTIONf_chiral_restr0.0431937
X-RAY DIFFRACTIONf_plane_restr0.0052313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.34520.4096490.39211088X-RAY DIFFRACTION29
3.3452-3.3930.4297640.37751263X-RAY DIFFRACTION33
3.393-3.44360.3376610.37281408X-RAY DIFFRACTION37
3.4436-3.49740.3696770.34991611X-RAY DIFFRACTION42
3.4974-3.55470.4063810.31621778X-RAY DIFFRACTION47
3.5547-3.6160.2991950.27681984X-RAY DIFFRACTION52
3.616-3.68170.31421140.27622126X-RAY DIFFRACTION56
3.6817-3.75250.30971110.27182344X-RAY DIFFRACTION61
3.7525-3.82910.28571160.25142522X-RAY DIFFRACTION67
3.8291-3.91230.27491280.25142727X-RAY DIFFRACTION70
3.9123-4.00330.24961360.24472812X-RAY DIFFRACTION74
4.0033-4.10330.25441470.2342990X-RAY DIFFRACTION79
4.1033-4.21420.25041570.21813187X-RAY DIFFRACTION84
4.2142-4.33820.2441640.21233472X-RAY DIFFRACTION91
4.3382-4.47810.26541770.21213603X-RAY DIFFRACTION95
4.4781-4.6380.21581770.20553741X-RAY DIFFRACTION98
4.638-4.82360.23481810.20153737X-RAY DIFFRACTION99
4.8236-5.04290.29951790.20253784X-RAY DIFFRACTION99
5.0429-5.30840.25471770.21343758X-RAY DIFFRACTION98
5.3084-5.64060.25921830.22133749X-RAY DIFFRACTION99
5.6406-6.07530.27521790.22773795X-RAY DIFFRACTION99
6.0753-6.68530.26991740.2363722X-RAY DIFFRACTION98
6.6853-7.64940.21341740.23373761X-RAY DIFFRACTION98
7.6494-9.62520.22171850.2083723X-RAY DIFFRACTION97
9.6252-48.56260.28131770.22843624X-RAY DIFFRACTION96

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