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- PDB-5yh2: The structure of DrFam20C1 and hFam20A complex -

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Basic information

Entry
Database: PDB / ID: 5yh2
TitleThe structure of DrFam20C1 and hFam20A complex
Components
  • Family with sequence similarity 20, member Ca
  • Pseudokinase FAM20A
KeywordsTRANSFERASE / complex / kinase
Function / homology
Function and homology information


tooth eruption / biomineral tissue development / phosphotransferase activity, alcohol group as acceptor / enamel mineralization / calcium ion homeostasis / protein serine/threonine kinase activator activity / 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) / positive regulation of protein phosphorylation ...tooth eruption / biomineral tissue development / phosphotransferase activity, alcohol group as acceptor / enamel mineralization / calcium ion homeostasis / protein serine/threonine kinase activator activity / 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) / positive regulation of protein phosphorylation / protein phosphorylation / protein serine/threonine kinase activity / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / membrane / cytoplasm
Similarity search - Function
FAM20, C-terminal / FAM20 / Golgi casein kinase, C-terminal, Fam20 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FAM20C golgi-associated secretory pathway kinase a / Pseudokinase FAM20A
Similarity search - Component
Biological speciesHomo sapiens (human)
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.55 Å
AuthorsZhang, H. / 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 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pseudokinase FAM20A
C: Family with sequence similarity 20, member Ca
B: Pseudokinase FAM20A
D: Family with sequence similarity 20, member Ca
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,9536
Polymers235,9394
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-36 kcal/mol
Surface area69550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.059, 110.059, 461.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 Family with sequence similarity 20, member Ca / DrFam20C1


Mass: 64505.363 Da / Num. of mol.: 2
Mutation: T223A, K421M, A422D, L423M, H425I, Y426F, S427D, L428F, K429L, T430M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: fam20ca / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: E7FBB8
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O13P3 / Details: ATP / 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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 11% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 8% w/v Polyethylene glycol 10,000

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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: 3.55→50 Å / Num. obs: 35615 / % possible obs: 100 % / Redundancy: 11.4 % / Net I/σ(I): 11

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.55→48.943 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.88
RfactorNum. reflection% reflection
Rfree0.2984 1556 5 %
Rwork0.2454 --
obs0.248 31136 87.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.55→48.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13431 0 62 0 13493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513846
X-RAY DIFFRACTIONf_angle_d0.73918758
X-RAY DIFFRACTIONf_dihedral_angle_d15.2178431
X-RAY DIFFRACTIONf_chiral_restr0.0442028
X-RAY DIFFRACTIONf_plane_restr0.0062410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5504-3.6650.3218620.29071169X-RAY DIFFRACTION39
3.665-3.79590.397780.29391493X-RAY DIFFRACTION50
3.7959-3.94780.35181200.29292288X-RAY DIFFRACTION77
3.9478-4.12740.34511570.29312973X-RAY DIFFRACTION99
4.1274-4.34490.3581580.26883000X-RAY DIFFRACTION100
4.3449-4.61690.28141600.24023037X-RAY DIFFRACTION100
4.6169-4.97310.26521600.21933051X-RAY DIFFRACTION100
4.9731-5.47290.28191610.2263062X-RAY DIFFRACTION100
5.4729-6.26350.28411630.23753076X-RAY DIFFRACTION100
6.2635-7.8860.28231660.23373161X-RAY DIFFRACTION100
7.886-48.94720.25821710.21693270X-RAY DIFFRACTION98

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