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- PDB-5jax: PKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B)... -

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Basic information

Entry
Database: PDB / ID: 5jax
TitlePKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP
ComponentscGMP-dependent protein kinase 1
Keywordstransferase/transferase inhibitor / Binding Sites / Cyclic AMP / Cyclic GMP / Cyclic GMP-Dependent Protein Kinase Type II / Mutagenesis / Site-Directed / Protein Binding / analogs / transferase-transferase inhibitor complex
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 / cGMP-mediated signaling / mitogen-activated protein kinase p38 binding / regulation of GTPase activity / 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-6J7 / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.486 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 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,5145
Polymers14,9871
Non-polymers5274
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-25 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.010, 47.010, 102.590
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-503-

HOH

21A-519-

HOH

31A-618-

HOH

41A-619-

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 219-351
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-6J7 / 2-amino-8-bromo-9-[(2R,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-1,9-dihydro-6H-purin-6-one / 8-Bromoguanosine 3',5'-cyclic monophosphate


Mass: 424.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11BrN5O7P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 1.94 Å3/Da / Density % sol: 36.76 %
Crystal growTemperature: 301 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: 8.2.2 / Wavelength: 0.99993 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 1.486→51.29 Å / Num. obs: 19769 / % possible obs: 99.9 % / Redundancy: 26.3 % / Rmerge(I) obs: 0.105 / Net I/av σ(I): 19.4 / Net I/σ(I): 0.999

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KU7
Resolution: 1.486→42.737 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.19
RfactorNum. reflection% reflection
Rfree0.199 1970 10 %
Rwork0.166 --
obs0.1693 19698 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.486→42.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 27 127 1145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091069
X-RAY DIFFRACTIONf_angle_d1.3221462
X-RAY DIFFRACTIONf_dihedral_angle_d11.088385
X-RAY DIFFRACTIONf_chiral_restr0.075164
X-RAY DIFFRACTIONf_plane_restr0.011185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4861-1.52320.2621370.24441232X-RAY DIFFRACTION100
1.5232-1.56440.25671390.22331244X-RAY DIFFRACTION100
1.5644-1.61050.22021360.20491237X-RAY DIFFRACTION100
1.6105-1.66240.22911390.20751241X-RAY DIFFRACTION100
1.6624-1.72190.21521370.20251233X-RAY DIFFRACTION100
1.7219-1.79080.22091390.1871247X-RAY DIFFRACTION100
1.7908-1.87230.24131380.18051249X-RAY DIFFRACTION100
1.8723-1.9710.20441390.17591256X-RAY DIFFRACTION100
1.971-2.09450.21121400.16111257X-RAY DIFFRACTION100
2.0945-2.25620.20311420.16111267X-RAY DIFFRACTION100
2.2562-2.48320.20191410.15831276X-RAY DIFFRACTION100
2.4832-2.84250.21551420.16531286X-RAY DIFFRACTION100
2.8425-3.5810.18691460.15761310X-RAY DIFFRACTION100
3.581-42.75440.16851550.14771393X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.5361-0.8547-1.75348.11170.5295.70690.0549-0.80240.250.5378-0.19970.1506-0.53220.00870.12360.2346-0.0009-0.0060.3439-0.06880.2093-3.591315.8411-2.3677
24.40062.9575-1.12413.4338-0.67320.70480.0064-0.24280.21730.1675-0.02180.0547-0.00340.00830.0150.10360.0066-0.00090.2164-0.03670.1354-4.106213.3376-8.6665
32.97020.23830.0832.56550.17123.101-0.0141-0.1746-0.17550.133-0.0116-0.00550.36710.02130.02280.09270.0279-0.00020.11830.00870.1-10.9761-0.7231-12.6579
43.37774.0957-0.51787.9592-3.2365.1514-0.00030.0105-0.9523-0.0423-0.0961-0.79070.54830.62130.08170.17030.0722-0.00160.22350.02440.3272.05311.6574-16.9953
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 257 )
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 339 )
4X-RAY DIFFRACTION4chain 'A' and (resid 340 through 351 )

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