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- PDB-5j48: PKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B)... -

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Basic information

Entry
Database: PDB / ID: 5j48
TitlePKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-pCPT-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 / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm ...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 / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle / Rap1 signalling / mitogen-activated protein kinase p38 binding / regulation of GTPase activity / cGMP-mediated signaling / dendrite development / cGMP effects / negative regulation of vascular associated smooth muscle cell proliferation / spermatid development / calcium channel regulator activity / cGMP binding / forebrain development / protein kinase A signaling / 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-6FW / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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
DepositionMar 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
B: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,53215
Polymers29,9732
Non-polymers1,55813
Water5,044280
1
A: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7467
Polymers14,9871
Non-polymers7596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7868
Polymers14,9871
Non-polymers7997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.510, 59.240, 67.320
Angle α, β, γ (deg.)90.00, 100.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 14986.738 Da / Num. of mol.: 2 / Fragment: unp residues 204-336
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

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Non-polymers , 5 types, 293 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-6FW / 2-amino-8-[(4-chlorophenyl)sulfanyl]-9-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-3,9-dihydro-6H-purin-6-one


Mass: 487.811 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15ClN5O7PS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 400, 200 mM CaAc, 0.1M NaAc pH 4.5-4.8 / PH range: 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: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.49→59.24 Å / Num. obs: 44551 / % possible obs: 99.1 % / Redundancy: 4.2 % / CC1/2: 0.852 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.1

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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

4ku7


Resolution: 1.49→34.952 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1891 1998 4.49 %
Rwork0.1634 --
obs0.1646 44528 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→34.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 97 280 2344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122150
X-RAY DIFFRACTIONf_angle_d1.2532904
X-RAY DIFFRACTIONf_dihedral_angle_d15.284745
X-RAY DIFFRACTIONf_chiral_restr0.084331
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.52730.29571390.25662974X-RAY DIFFRACTION97
1.5273-1.56860.2451410.22583017X-RAY DIFFRACTION99
1.5686-1.61470.22451430.20183033X-RAY DIFFRACTION99
1.6147-1.66690.22161430.18933021X-RAY DIFFRACTION99
1.6669-1.72640.21271420.18633037X-RAY DIFFRACTION99
1.7264-1.79560.19131430.17843045X-RAY DIFFRACTION99
1.7956-1.87730.17821430.16593040X-RAY DIFFRACTION99
1.8773-1.97620.18881420.16263041X-RAY DIFFRACTION99
1.9762-2.10.17981430.1493037X-RAY DIFFRACTION99
2.1-2.26220.16661420.14153019X-RAY DIFFRACTION99
2.2622-2.48980.16281430.14613043X-RAY DIFFRACTION99
2.4898-2.84990.17291440.14843056X-RAY DIFFRACTION100
2.8499-3.590.18451440.15063074X-RAY DIFFRACTION99
3.59-34.96170.19571460.1683093X-RAY DIFFRACTION98
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)
14.68811.96861.2161.05811.1151.9102-0.0129-0.0227-0.2159-0.00580.0459-0.11170.24490.0919-0.02360.16790.01210.02150.0822-0.01030.164514.6536-7.9562-37.9025
21.5863-0.2818-0.31482.85170.26963.429-0.0392-0.01950.0055-0.08740.00220.05330.04-0.03610.01660.0834-0.00780.0120.0633-0.00430.12912.8168.7287-28.1533
33.70321.94922.72371.02511.43322.00160.3760.13-0.0390.0744-0.2764-0.34080.15170.2656-0.10110.36210.01560.07650.45420.12880.399622.2044-0.2814-21.7439
46.6959-1.9810.63122.7927-0.26542.1287-0.10920.0334-0.12530.08210.08460.0940.2417-0.05680.01590.1319-0.00430.02990.05010.01310.1268-7.992-14.41794.7225
51.83130.8491-0.23873.5704-1.86434.0905-0.0175-0.011-0.00070.0378-0.0233-0.317-0.02290.16690.05470.06180.0080.00570.0563-0.00140.1149-4.88053.6108-2.191
63.23990.1036-0.82814.2733-1.64035.0993-0.06750.34560.12-0.37330.13910.0589-0.0199-0.1378-0.05270.0899-0.0414-0.0170.111-0.00140.0883-10.85275.5863-10.2146
71.2675-0.73370.77496.43740.74782.02660.07680.132-0.1582-0.1378-0.0603-0.0990.2477-0.0128-0.02890.0971-0.01260.03260.10630.00020.1343-5.466-4.1472-4.0918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 217 through 251 )
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 339 )
3X-RAY DIFFRACTION3chain 'A' and (resid 340 through 351 )
4X-RAY DIFFRACTION4chain 'B' and (resid 217 through 251 )
5X-RAY DIFFRACTION5chain 'B' and (resid 252 through 285 )
6X-RAY DIFFRACTION6chain 'B' and (resid 286 through 318 )
7X-RAY DIFFRACTION7chain 'B' and (resid 319 through 343 )

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