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- PDB-5jd7: PKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B... -

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Basic information

Entry
Database: PDB / ID: 5jd7
TitlePKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with PET-cGMP
ComponentscGMP-dependent protein kinase 1
KeywordsPROTEIN BINDING / Binding Sites / Cyclic AMP / Cyclic GMP / Cyclic GMP-Dependent Protein Kinase Type II / Mutagenesis / Site-Directed / analogs
Function / homology
Function and homology information


negative regulation of inositol phosphate biosynthetic process / negative regulation of glutamate secretion / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of vascular associated smooth muscle cell migration / negative regulation of platelet aggregation / relaxation of vascular associated smooth muscle ...negative regulation of inositol phosphate biosynthetic process / negative regulation of glutamate secretion / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of vascular associated smooth muscle cell migration / negative regulation of platelet aggregation / relaxation of vascular associated smooth muscle / positive regulation of circadian rhythm / Rap1 signalling / mitogen-activated protein kinase p38 binding / regulation of GTPase activity / cGMP-mediated signaling / dendrite development / spermatid development / cGMP effects / negative regulation of vascular associated smooth muscle cell proliferation / calcium channel regulator activity / cGMP binding / forebrain development / cerebellum development / acrosomal vesicle / neuron migration / sarcolemma / Ca2+ pathway / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / protein kinase activity / protein phosphorylation / protein serine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / 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. ...cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / 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 / Extension to Ser/Thr-type protein kinases / Jelly Rolls / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6JR / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å
AuthorsCampbell, J.C. / Sankaran, B. / Kim, C.W.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structural Basis of Analog Specificity in PKG I and II.
Authors: Campbell, J.C. / Henning, P. / Franz, E. / Sankaran, B. / Herberg, F.W. / Kim, C.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4322
Polymers14,9871
Non-polymers4451
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.290, 46.290, 102.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

21A-576-

HOH

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Components

#1: Protein cGMP-dependent protein kinase 1 / cGK1 / cGMP-dependent protein kinase I / cGKI


Mass: 14986.738 Da / Num. of mol.: 1 / Fragment: UNP residues 219-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q13976, cGMP-dependent protein kinase
#2: Chemical ChemComp-6JR / 3-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-6-phenyl-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one / PET-cGMP


Mass: 445.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N5O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.72 Å3/Da / Density % sol: 32.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 400, 200 mM CaAc, 0.1M NaAc pH 4.5-4.8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.749→42.185 Å / Num. obs: 11850 / % possible obs: 99.57 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.2

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ku7

4ku7


Resolution: 1.749→42.185 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 1185 10 %
Rwork0.1934 --
obs0.1967 11850 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.749→42.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 31 80 1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121047
X-RAY DIFFRACTIONf_angle_d1.0961428
X-RAY DIFFRACTIONf_dihedral_angle_d13.308604
X-RAY DIFFRACTIONf_chiral_restr0.062162
X-RAY DIFFRACTIONf_plane_restr0.007180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.749-1.82860.29881430.2711287X-RAY DIFFRACTION99
1.8286-1.9250.28661450.25841307X-RAY DIFFRACTION100
1.925-2.04560.32421440.23371296X-RAY DIFFRACTION100
2.0456-2.20350.27731470.21281321X-RAY DIFFRACTION100
2.2035-2.42530.18871460.19821315X-RAY DIFFRACTION100
2.4253-2.77610.25161480.19251326X-RAY DIFFRACTION100
2.7761-3.49740.20621510.18761356X-RAY DIFFRACTION100
3.4974-42.19690.19921610.17011457X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.10472.3813-2.2416.0996-2.87364.7479-0.0812-0.5180.0991.3387-0.2288-0.3892-0.24030.43850.44550.54950.015-0.09950.2375-0.00970.277115.50183.20823.2044
22.0526-3.5742-4.39813.43421.77864.19280.3146-0.5877-0.62220.4783-0.16180.38630.6852-0.1116-0.08640.3628-0.0074-0.03280.22910.07870.25789.6789-4.242216.9732
31.4796-2.0121-0.23394.64470.20930.2195-0.1768-0.0740.5670.4903-0.0234-0.7397-0.56590.11540.06580.4628-0.0018-0.11810.1468-0.03060.269814.78337.644516.8573
42.3315-0.51360.88091.5635-0.62693.1204-0.1623-0.32460.20160.39870.06460.1104-0.5071-0.40290.08810.3240.04130.0350.2026-0.0310.23490.74214.639414.1873
54.84990.11682.35563.1066-1.40745.2381-0.6339-0.6727-0.46110.58270.61410.9322-0.6244-1.0926-0.06380.31290.06860.19330.58630.08570.3596-10.361210.513615.7434
62.3589-1.42920.75643.2001-0.35112.4612-0.0856-0.1047-0.24830.27730.03130.25680.1091-0.17280.04230.2069-0.04190.03170.15090.02190.20633.10386.416210.5297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 222 through 233 )
2X-RAY DIFFRACTION2chain 'A' and (resid 234 through 241 )
3X-RAY DIFFRACTION3chain 'A' and (resid 242 through 257 )
4X-RAY DIFFRACTION4chain 'A' and (resid 258 through 278 )
5X-RAY DIFFRACTION5chain 'A' and (resid 279 through 299 )
6X-RAY DIFFRACTION6chain 'A' and (resid 300 through 351 )

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