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- PDB-4f9k: Crystal Structure of human cAMP-dependent protein kinase type I-b... -

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Basic information

Entry
Database: PDB / ID: 4f9k
TitleCrystal Structure of human cAMP-dependent protein kinase type I-beta regulatory subunit (fragment 11-73), Northeast Structural Genomics Consortium (NESG) Target HR8613A
ComponentscAMP-dependent protein kinase type I-beta regulatory subunitCAMP-dependent pathway
KeywordsTransferase Regulator / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


positive regulation of fear response / regulation of synaptic vesicle cycle / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / cAMP-dependent protein kinase inhibitor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / cAMP-dependent protein kinase complex / protein kinase A catalytic subunit binding ...positive regulation of fear response / regulation of synaptic vesicle cycle / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / cAMP-dependent protein kinase inhibitor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / cAMP-dependent protein kinase complex / protein kinase A catalytic subunit binding / positive regulation of excitatory postsynaptic potential / PKA activation in glucagon signalling / DARPP-32 events / Hedgehog 'off' state / cAMP binding / hippocampal mossy fiber to CA3 synapse / multivesicular body / FCGR3A-mediated IL10 synthesis / positive regulation of long-term synaptic potentiation / Schaffer collateral - CA1 synapse / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / postsynapse / learning or memory / protein phosphorylation / glutamatergic synapse / plasma membrane / cytosol
Similarity search - Function
RIbeta, dimerization/docking domain / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site ...RIbeta, dimerization/docking domain / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
cAMP-dependent protein kinase type I-beta regulatory subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsKuzin, A. / Lew, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Shastry, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Lew, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Shastry, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of human cAMP-dependent protein kinase type I-beta regulatory subunit (fragment 11-73), Northeast Structural Genomics Consortium (NESG) Target HR8613A
Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Shastry, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase type I-beta regulatory subunit
B: cAMP-dependent protein kinase type I-beta regulatory subunit
C: cAMP-dependent protein kinase type I-beta regulatory subunit
D: cAMP-dependent protein kinase type I-beta regulatory subunit


Theoretical massNumber of molelcules
Total (without water)46,6394
Polymers46,6394
Non-polymers00
Water0
1
A: cAMP-dependent protein kinase type I-beta regulatory subunit
B: cAMP-dependent protein kinase type I-beta regulatory subunit


Theoretical massNumber of molelcules
Total (without water)23,3202
Polymers23,3202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-26 kcal/mol
Surface area8240 Å2
MethodPISA
2
C: cAMP-dependent protein kinase type I-beta regulatory subunit
D: cAMP-dependent protein kinase type I-beta regulatory subunit


Theoretical massNumber of molelcules
Total (without water)23,3202
Polymers23,3202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-30 kcal/mol
Surface area8050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.270, 50.070, 75.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
cAMP-dependent protein kinase type I-beta regulatory subunit / CAMP-dependent pathway


Mass: 11659.776 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: P31321

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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: 1.67 Å3/Da / Density % sol: 26.32 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 6.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.2M (NH4)2SO4, 0.1M Na-c, microbatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 24, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 13955 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 56.63 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassificationNB
PHENIXdev_988refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.3 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.658 / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.324 362 4.59 %random
Rwork0.254 ---
obs0.257 7880 97.12 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.673 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 217.66 Å2 / Biso mean: 69.173 Å2 / Biso min: 33.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.425 Å2-0 Å20 Å2
2---0.659 Å2-0 Å2
3---1.084 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 0 0 1906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121938
X-RAY DIFFRACTIONf_angle_d1.4752573
X-RAY DIFFRACTIONf_chiral_restr0.09276
X-RAY DIFFRACTIONf_plane_restr0.004331
X-RAY DIFFRACTIONf_dihedral_angle_d21.036791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-3.2050.4361170.3272382249995
3.205-4.0360.3451190.2412517263699
4.036-29.3020.2781260.2392619274598
Refinement TLS params.Method: refined / Origin x: 18.0303 Å / Origin y: 15.17 Å / Origin z: 33.1361 Å
111213212223313233
T0.4869 Å2-0.0133 Å20.0148 Å2-0.3613 Å2-0.0252 Å2--0.4443 Å2
L0.7187 °2-0.0164 °20.5319 °2-0.0718 °2-0.5275 °2--3.0099 °2
S0.1221 Å °0.0187 Å °0.1325 Å °0.0788 Å °-0.0809 Å °-0.003 Å °0.3648 Å °-0.0647 Å °0.005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 72
2X-RAY DIFFRACTION1allB16 - 73
3X-RAY DIFFRACTION1allC16 - 73
4X-RAY DIFFRACTION1allD16 - 70

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