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- PDB-3h4j: crystal structure of pombe AMPK KDAID fragment -

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Basic information

Entry
Database: PDB / ID: 3h4j
Titlecrystal structure of pombe AMPK KDAID fragment
ComponentsSNF1-like protein kinase ssp2
KeywordsTRANSFERASE / AMPK / kinase / ATP-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


positive regulation of ascus development / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine shuttle / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / mitotic spindle pole body / SREBP signaling pathway ...positive regulation of ascus development / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine shuttle / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / mitotic spindle pole body / SREBP signaling pathway / CAMKK-AMPK signaling cascade / nucleotide-activated protein kinase complex / negative regulation of cytoplasmic translation / negative regulation of TORC1 signaling / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Helicase, Ruva Protein; domain 3 / Phosphorylase Kinase; domain 1 ...Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Helicase, Ruva Protein; domain 3 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
SNF1-like protein kinase ssp2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, L. / Jiao, Z.-H. / Zheng, L.-S. / Zhang, Y.-Y. / Xie, S.-T. / Wang, Z.-X. / Wu, J.-W.
CitationJournal: Nature / Year: 2009
Title: Structural insight into the autoinhibition mechanism of AMP-activated protein kinase
Authors: Chen, L. / Jiao, Z.-H. / Zheng, L.-S. / Zhang, Y.-Y. / Xie, S.-T. / Wang, Z.-X. / Wu, J.-W.
History
DepositionApr 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: SNF1-like protein kinase ssp2
A: SNF1-like protein kinase ssp2


Theoretical massNumber of molelcules
Total (without water)77,9762
Polymers77,9762
Non-polymers00
Water1,874104
1
B: SNF1-like protein kinase ssp2


Theoretical massNumber of molelcules
Total (without water)38,9881
Polymers38,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SNF1-like protein kinase ssp2


Theoretical massNumber of molelcules
Total (without water)38,9881
Polymers38,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-38 kcal/mol
Surface area31120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.964, 128.964, 106.872
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein SNF1-like protein kinase ssp2 / AMPK KDAID


Mass: 38987.988 Da / Num. of mol.: 2 / Fragment: UNP residues 25-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: SPQ-01 / Gene: ssp2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O74536, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate, pH 5.6, 1.2M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 27824 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 71.11 Å2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EUE

2eue
PDB Unreleased entry


Resolution: 2.8→39.262 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.759 / SU ML: 0.39 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1256 5.04 %random
Rwork0.218 ---
obs0.22 24921 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.756 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 294.06 Å2 / Biso mean: 102.318 Å2 / Biso min: 31.81 Å2
Baniso -1Baniso -2Baniso -3
1--10.93 Å20 Å20 Å2
2---10.93 Å2-0 Å2
3---17.675 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 0 104 5364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015373
X-RAY DIFFRACTIONf_angle_d1.8457254
X-RAY DIFFRACTIONf_chiral_restr0.219795
X-RAY DIFFRACTIONf_plane_restr0.007937
X-RAY DIFFRACTIONf_dihedral_angle_d20.6312029
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.9120.3861330.28126152748100
2.912-3.0450.3431420.27126172759100
3.045-3.2050.3581280.27726292757100
3.205-3.4060.3321310.27226352766100
3.406-3.6680.2661400.24626252765100
3.668-4.0370.2491440.20126192763100
4.037-4.6210.2191500.18226302780100
4.621-5.8190.2141440.18826282772100
5.819-39.2650.2381440.1972667281199

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