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- PDB-6bq8: Joint X-ray/neutron structure of PKG II CNB-B domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 6bq8
TitleJoint X-ray/neutron structure of PKG II CNB-B domain in complex with 8-pCPT-cGMP
ComponentscGMP-dependent protein kinase 2
KeywordsTransferase / SIGNALING PROTEIN / protein kinase G / regulatory domain / neutron crystallography / activator / hydrogen bonding / protonation state
Function / homology
Function and homology information


negative regulation of chloride transport / tetrahydrobiopterin metabolic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / positive regulation of chondrocyte differentiation / mitogen-activated protein kinase binding / positive regulation of protein localization / cGMP effects / cGMP binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation ...negative regulation of chloride transport / tetrahydrobiopterin metabolic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / positive regulation of chondrocyte differentiation / mitogen-activated protein kinase binding / positive regulation of protein localization / cGMP effects / cGMP binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / protein localization to plasma membrane / RAS processing / Ca2+ pathway / nuclear membrane / protein kinase activity / apical plasma membrane / protein phosphorylation / protein serine kinase activity / signal transduction / ATP binding / identical protein binding / cytosol
Similarity search - Function
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 ...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
DEUTERATED WATER / STRONTIUM ION / Chem-WNU / cGMP-dependent protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, C. / Kovalevsky, A. / Gerlits, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM090161 United States
Citation
Journal: Biochemistry / Year: 2018
Title: Neutron Crystallography Detects Differences in Protein Dynamics: Structure of the PKG II Cyclic Nucleotide Binding Domain in Complex with an Activator.
Authors: Gerlits, O. / Campbell, J.C. / Blakeley, M.P. / Kim, C. / Kovalevsky, A.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2009
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
History
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0May 10, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 3.0May 17, 2023Group: Non-polymer description / Category: chem_comp / Item: _chem_comp.formula
Revision 3.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0884
Polymers17,3941
Non-polymers6943
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-8 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.650, 51.300, 68.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cGMP-dependent protein kinase 2 / cGK2 / cGMP-dependent protein kinase II / cGKII


Mass: 17394.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG2, PRKGR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13237, cGMP-dependent protein kinase
#2: Chemical ChemComp-WNU / 2-(~2~H_2_)amino-8-[(4-chlorophenyl)sulfanyl]-9-[(2S,4aR,6R,7R,7aS)-2-hydroxy-7-(~2~H)hydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl](~2~H)-1,9-dihydro-6H-purin-6-one


Mass: 487.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15ClN5O7PS
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 30% MPD, 20 mM SrCl2, 100 mM NaOAc pH 4.6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
NUCLEAR REACTORILL LADI III22.8-4.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATENov 1, 2015OSMIC VARIMAX
MAATEL IMAGINE2IMAGE PLATENov 26, 2015COLLIMATORS
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
22.81
341
Reflection

Entry-ID: 6BQ8

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2-101049297.33.30.064112.5
2.2-40596674.73.60.14127.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.063.20.5352.8197.6
2.2-2.322.40.194.5251.9

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Processing

Software
NameVersionClassification
nCNS1.0.0refinement
LAUEGENdata reduction
LSCALEdata scaling
PHASERphasing
Refinement

Biso mean: 38.16 Å2 / % reflection Rfree: 5 % / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / σ(F): 2 / Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 5BV6

5bv6

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection obs% reflection obs (%)
2-10X-RAY DIFFRACTION0.2450.1994871040196
2.2-40NEUTRON DIFFRACTION0.2880.232287594972.6
Refine analyze
Refine-ID#notag 0Luzzati coordinate error free (Å)Luzzati sigma a free (Å)
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.40.31
Luzzati d res low-5
Luzzati sigma a0.690.5
NEUTRON DIFFRACTION0.270.23
Refine funct minimized
Refine-IDType
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
X-RAY DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 40 40 1294
LS refinement shell

Rfactor Rfree error: 0.049 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.2925950.2961304X-RAY DIFFRACTION93.3
2.2-2.310.4772450.361996NEUTRON DIFFRACTION49.4

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