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- PDB-1cja: ACTIN-FRAGMIN KINASE, CATALYTIC DOMAIN FROM PHYSARUM POLYCEPHALUM -

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Basic information

Entry
Database: PDB / ID: 1cja
TitleACTIN-FRAGMIN KINASE, CATALYTIC DOMAIN FROM PHYSARUM POLYCEPHALUM
ComponentsPROTEIN (ACTIN-FRAGMIN KINASE)
KeywordsTRANSFERASE / KINASE / ACTIN
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / cytoplasm
Similarity search - Function
Actin-fragmin kinase, catalytic domain / Actin-fragmin kinase, catalytic / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Kelch-type beta propeller / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Protein kinase-like domain superfamily / 2-Layer Sandwich ...Actin-fragmin kinase, catalytic domain / Actin-fragmin kinase, catalytic / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Kelch-type beta propeller / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Actin-fragmin kinase / Actin-fragmin kinase
Similarity search - Component
Biological speciesPhysarum polycephalum (eukaryote)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.9 Å
AuthorsSteinbacher, S. / Hof, P. / Eichinger, L. / Schleicher, M. / Gettemans, J. / Vandekerckhove, J. / Huber, R. / Benz, J.
CitationJournal: EMBO J. / Year: 1999
Title: The crystal structure of the Physarum polycephalum actin-fragmin kinase: an atypical protein kinase with a specialized substrate-binding domain.
Authors: Steinbacher, S. / Hof, P. / Eichinger, L. / Schleicher, M. / Gettemans, J. / Vandekerckhove, J. / Huber, R. / Benz, J.
History
DepositionApr 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ACTIN-FRAGMIN KINASE)
B: PROTEIN (ACTIN-FRAGMIN KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8944
Polymers76,1992
Non-polymers6942
Water0
1
A: PROTEIN (ACTIN-FRAGMIN KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4472
Polymers38,1001
Non-polymers3471
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (ACTIN-FRAGMIN KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4472
Polymers38,1001
Non-polymers3471
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.900, 178.900, 59.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.980112, 0.006834, 0.198328), (-0.043666, -0.982339, -0.181941), (0.193582, -0.186983, 0.963101)
Vector: 61.657, 123.451, 5.988)

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Components

#1: Protein PROTEIN (ACTIN-FRAGMIN KINASE)


Mass: 38099.562 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94706, UniProt: P80197*PLUS
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*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: 3.59 Å3/Da / Density % sol: 68 %
Crystal growpH: 6 / Details: 2.0 M LI2SO4, 0.1 M MES, PH 6.0
Crystal grow
*PLUS
pH: 7.5 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
27.1 mg/mlprotein11
32.9 mMAMP11
40.6 M11Li2SO4
536 mMMES/NaOH11
62.0 M12Li2SO4

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. all: 23306 / Num. obs: 23306 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08
Reflection shellResolution: 2.9→3.06 Å / Rmerge(I) obs: 0.419 / Rsym value: 0.419 / % possible all: 77.4
Reflection
*PLUS
Lowest resolution: 15 Å / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 77.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: SIR / Resolution: 2.9→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.272 -5 %RANDOM
Rwork0.198 ---
obs-22289 90.8 %-
Displacement parametersBiso mean: 55.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6246 0 46 0 6292
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.82
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 55.1 Å2

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