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- PDB-5mhi: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5mhi
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule (5-chloro-2-methoxyphenyl)methanamine
Components(cAMP-dependent protein kinase ...Protein kinase A) x 2
KeywordsTRANSFERASE / fragment / complex / serine threonine kinase / cAMP / kinase / PKA
Function / homology
Function and homology information


regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / protein kinase A catalytic subunit binding / plasma membrane raft / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cellular response to heat / manganese ion binding / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / phosphorylation / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / glutamatergic synapse / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / magnesium ion binding / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
(5-chloranyl-2-methoxy-phenyl)methylazanium / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.489 Å
AuthorsSiefker, C. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: A crystallographic fragment study with cAMP-dependent protein kinase A
Authors: Siefker, C. / Heine, A. / Klebe, G.
History
DepositionNov 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 2.0Feb 21, 2018Group: Atomic model / Non-polymer description / Structure summary
Category: atom_site / entity
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _chem_comp.formula / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description
Revision 2.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase inhibitor alpha-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6496
Polymers43,1072
Non-polymers5424
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-14 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.341, 72.594, 108.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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CAMP-dependent protein kinase ... , 2 types, 2 molecules AB

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / CAMP-dependent pathway / PKA C-alpha


Mass: 41113.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor alpha-like protein / CAMP-dependent pathway


Mass: 1993.318 Da / Num. of mol.: 1 / Fragment: UNP residues 12-30 / Source method: obtained synthetically / Details: cAMP-dependent protein kinase inhibitory peptide / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: A0A061IH64*PLUS

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Non-polymers , 4 types, 307 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-7N9 / (5-chloranyl-2-methoxy-phenyl)methylazanium


Mass: 172.632 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11ClNO
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: MES-BIS-TRIS Mega8-solution DTT EDTA LiCl Methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2016 / Details: Silicon, active surface 50 nm Rh-coated
RadiationMonochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.489→50 Å / Num. obs: 76142 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 1 / Rsym value: 0.038 / Net I/σ(I): 26.1
Reflection shellResolution: 1.489→1.58 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 3.7 / CC1/2: 0.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WIH

4wih


Resolution: 1.489→45.475 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1647 3807 5 %
Rwork0.1469 --
obs0.1478 76135 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.489→45.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 30 303 3194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083143
X-RAY DIFFRACTIONf_angle_d0.9744285
X-RAY DIFFRACTIONf_dihedral_angle_d201143
X-RAY DIFFRACTIONf_chiral_restr0.075453
X-RAY DIFFRACTIONf_plane_restr0.007573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4886-1.50750.20811340.17012560X-RAY DIFFRACTION97
1.5075-1.52730.20461400.15592652X-RAY DIFFRACTION100
1.5273-1.54820.18461400.14622658X-RAY DIFFRACTION100
1.5482-1.57030.18321370.13952608X-RAY DIFFRACTION100
1.5703-1.59380.18241400.13872658X-RAY DIFFRACTION100
1.5938-1.61870.1721400.12812669X-RAY DIFFRACTION100
1.6187-1.64520.15631400.12782658X-RAY DIFFRACTION100
1.6452-1.67360.16041390.12392635X-RAY DIFFRACTION100
1.6736-1.7040.15411400.12242655X-RAY DIFFRACTION100
1.704-1.73680.17291400.12222668X-RAY DIFFRACTION100
1.7368-1.77230.1421400.11992657X-RAY DIFFRACTION100
1.7723-1.81080.19391400.12222666X-RAY DIFFRACTION100
1.8108-1.85290.17361400.12522648X-RAY DIFFRACTION100
1.8529-1.89930.1581400.13432670X-RAY DIFFRACTION100
1.8993-1.95060.15281410.13782676X-RAY DIFFRACTION100
1.9506-2.0080.15871410.1342672X-RAY DIFFRACTION100
2.008-2.07280.16781410.13942681X-RAY DIFFRACTION100
2.0728-2.14690.18191400.13882667X-RAY DIFFRACTION100
2.1469-2.23290.1761410.13312679X-RAY DIFFRACTION100
2.2329-2.33450.1491420.12862703X-RAY DIFFRACTION100
2.3345-2.45760.15451410.13072680X-RAY DIFFRACTION100
2.4576-2.61150.1661420.13782696X-RAY DIFFRACTION100
2.6115-2.81310.14971430.14562705X-RAY DIFFRACTION100
2.8131-3.09620.15191430.15042719X-RAY DIFFRACTION100
3.0962-3.5440.17531430.16312721X-RAY DIFFRACTION100
3.544-4.46450.15611460.14832777X-RAY DIFFRACTION100
4.4645-45.49650.17291530.18182890X-RAY DIFFRACTION100

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