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- PDB-6bdl: Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ia... -

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Basic information

Entry
Database: PDB / ID: 6bdl
TitleCrystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain in apo state
ComponentscGMP-dependent protein kinase 1
KeywordsTRANSFERASE / Serine/threonine protein kinases (EC 2.7.11.12)
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 / 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 / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / 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 / cGMP effects / negative regulation of vascular associated smooth muscle cell proliferation / cGMP binding / spermatid development / calcium channel regulator activity / 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 / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / 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
IMIDAZOLE / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsQin, L. / Sankaran, B. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM090161-08 United States
CitationJournal: to be published
Title: Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain
Authors: Qin, L. / Sankaran, B. / Casteel, D. / Kim, C.
History
DepositionOct 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
B: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0864
Polymers78,9482
Non-polymers1382
Water8,431468
1
A: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5432
Polymers39,4741
Non-polymers691
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)39,5432
Polymers39,4741
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.114, 50.879, 85.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-876-

HOH

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Components

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


Mass: 39473.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Plasmid: pBlueBacHis2A / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13976, cGMP-dependent protein kinase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M PCTP, pH6.0, 25% w/v PEG1500

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.96→38.1 Å / Num. obs: 52831 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.2
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3706 / CC1/2: 0.841 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIX1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FJQ

3fjq


Resolution: 1.96→38.1 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 2017 3.82 %
Rwork0.2087 --
obs0.2092 52825 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 10 468 5679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055341
X-RAY DIFFRACTIONf_angle_d0.6777227
X-RAY DIFFRACTIONf_dihedral_angle_d19.8351920
X-RAY DIFFRACTIONf_chiral_restr0.048779
X-RAY DIFFRACTIONf_plane_restr0.005928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0090.36371500.29213606X-RAY DIFFRACTION100
2.009-2.06330.32291380.28273590X-RAY DIFFRACTION100
2.0633-2.12410.31341450.26383653X-RAY DIFFRACTION100
2.1241-2.19260.28241360.25553597X-RAY DIFFRACTION100
2.1926-2.2710.2591400.26583596X-RAY DIFFRACTION100
2.271-2.36190.26881460.25263656X-RAY DIFFRACTION100
2.3619-2.46930.27621420.23643603X-RAY DIFFRACTION100
2.4693-2.59950.26051430.24423627X-RAY DIFFRACTION100
2.5995-2.76230.24791470.23443619X-RAY DIFFRACTION100
2.7623-2.97550.23111440.2253637X-RAY DIFFRACTION100
2.9755-3.27480.23041470.22123622X-RAY DIFFRACTION100
3.2748-3.74830.19291440.19433634X-RAY DIFFRACTION100
3.7483-4.72110.16241470.163679X-RAY DIFFRACTION100
4.7211-38.10730.1831480.16883689X-RAY DIFFRACTION98

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