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- PDB-4nt4: Crystal structure of the kinase domain of Gilgamesh isoform I fro... -

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Basic information

Entry
Database: PDB / ID: 4nt4
TitleCrystal structure of the kinase domain of Gilgamesh isoform I from Drosophila melanogaster
ComponentsGilgamesh, isoform I
KeywordsTRANSFERASE / Serine/threonine protein kinase / Wnt signaling pathway
Function / homology
Function and homology information


sperm individualization complex / negative regulation of actin nucleation / regulation of endocytic recycling / sperm individualization / glial cell migration / olfactory learning / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase ...sperm individualization complex / negative regulation of actin nucleation / regulation of endocytic recycling / sperm individualization / glial cell migration / olfactory learning / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Casein kinase 1 gamma C-terminal / Casein kinase 1 gamma C terminal / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Casein kinase 1 gamma C-terminal / Casein kinase 1 gamma C terminal / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsChen, C.C. / Shi, Z.B. / Zhou, Z.C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of the kinase domain of Gilgamesh from Drosophila melanogaster
Authors: Han, N. / Chen, C. / Shi, Z. / Cheng, D.
History
DepositionNov 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gilgamesh, isoform I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7064
Polymers36,4221
Non-polymers2843
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Gilgamesh, isoform I
hetero molecules

A: Gilgamesh, isoform I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4138
Polymers72,8442
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area3480 Å2
ΔGint-52 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.025, 52.025, 291.727
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Gilgamesh, isoform I / LD28216p


Mass: 36422.047 Da / Num. of mol.: 1 / Fragment: UNP residues 55-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG6963, Dmel_CG6963, gish / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codonplus
References: UniProt: Q86NK8, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 289 K / pH: 7
Details: 1% trypton, 50mM HEPES pH 7.0, 9% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 9124 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 85.69 Å2 / Net I/σ(I): 16.2
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZR

2izr


Resolution: 2.86→36.79 Å / SU ML: 0.48 / σ(F): 1.34 / Phase error: 33.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.296 907 10 %
Rwork0.254 --
obs0.258 9074 89.8 %
all-10107 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.86→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 16 9 2360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032429
X-RAY DIFFRACTIONf_angle_d0.7513285
X-RAY DIFFRACTIONf_dihedral_angle_d13.452863
X-RAY DIFFRACTIONf_chiral_restr0.027350
X-RAY DIFFRACTIONf_plane_restr0.002424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-3.03850.4381500.37741347X-RAY DIFFRACTION92
3.0385-3.2730.3761610.33641455X-RAY DIFFRACTION99
3.273-3.60210.38031610.30521443X-RAY DIFFRACTION98
3.6021-4.12270.2923950.2526851X-RAY DIFFRACTION56
4.1227-5.19180.28071650.22921480X-RAY DIFFRACTION97
5.1918-36.79030.25521750.2261591X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 61.8234 Å / Origin y: 29.7492 Å / Origin z: 15.9674 Å
111213212223313233
T0.3428 Å20.0698 Å20.087 Å2-0.6841 Å2-0.1004 Å2--0.5834 Å2
L2.6364 °2-0.9121 °2-0.7454 °2-4.3404 °22.0723 °2--3.9313 °2
S0.2393 Å °-0.1415 Å °0.2914 Å °-0.2175 Å °-0.492 Å °0.0982 Å °-0.0181 Å °-0.4338 Å °0.1701 Å °
Refinement TLS groupSelection details: all

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