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- PDB-5jix: PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-... -

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Basic information

Entry
Database: PDB / ID: 5jix
TitlePKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP
ComponentscGMP-dependent protein kinase 2
KeywordsTRANSFERASE / Cyclic GMP-Dependent Protein Kinase Type II
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
Chem-6J7 / cGMP-dependent protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsCampbell, J.C. / 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 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,71113
Polymers17,3941
Non-polymers1,31612
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.620, 52.090, 68.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 131 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: 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


Mass: 424.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11BrN5O7P
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
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: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.47→41.494 Å / Num. obs: 25594 / % possible obs: 98.17 % / Redundancy: 7.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5bv6

5bv6


Resolution: 1.47→41.494 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.54
RfactorNum. reflection% reflection
Rfree0.1879 1998 7.81 %
Rwork0.1647 --
obs0.1665 25594 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.47→41.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 76 119 1360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091249
X-RAY DIFFRACTIONf_angle_d1.3051672
X-RAY DIFFRACTIONf_dihedral_angle_d14.078466
X-RAY DIFFRACTIONf_chiral_restr0.073182
X-RAY DIFFRACTIONf_plane_restr0.006209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4701-1.50690.41371170.35641401X-RAY DIFFRACTION83
1.5069-1.54760.35441360.31521586X-RAY DIFFRACTION93
1.5476-1.59320.25361420.25611686X-RAY DIFFRACTION99
1.5932-1.64460.25211410.22031671X-RAY DIFFRACTION100
1.6446-1.70340.22551440.19861689X-RAY DIFFRACTION100
1.7034-1.77160.21311430.18281688X-RAY DIFFRACTION100
1.7716-1.85220.20181440.17281702X-RAY DIFFRACTION100
1.8522-1.94980.16671440.15721698X-RAY DIFFRACTION100
1.9498-2.0720.17171440.13921706X-RAY DIFFRACTION100
2.072-2.2320.16531460.12711713X-RAY DIFFRACTION100
2.232-2.45650.14741460.13331730X-RAY DIFFRACTION100
2.4565-2.81190.17431460.13991720X-RAY DIFFRACTION100
2.8119-3.54250.16031490.15591759X-RAY DIFFRACTION100
3.5425-41.51080.19721560.16871847X-RAY DIFFRACTION100
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)
10.1427-0.57330.17584.7939-0.80750.25360.13980.07080.3419-0.3489-0.1055-0.42550.08320.1154-0.00760.18170.00040.03080.24070.00810.2477-4.975612.9545-20.0331
20.9166-0.2674-0.6140.59790.2341.1640.02860.0879-0.02030.0178-0.0661-0.0077-0.0109-0.03190.030.11430.00430.00790.1083-0.00430.1116-11.54387.6111-20.4491
32.0060.6990.17141.75160.542.42960.0447-0.094-0.01570.0993-0.04150.2216-0.2982-0.29330.00270.20580.04290.01570.19380.02060.191-25.95657.293-6.1658
41.40730.8773-0.27561.3162-0.37561.3494-0.0232-0.06470.03640.0795-0.0085-0.0852-0.11360.07370.03360.14310.0056-0.00710.15180.00490.1706-16.78235.729-5.4499
51.39630.0958-0.04171.19480.01391.3872-0.0215-0.1817-0.06030.2379-0.00460.07760.06320.06180.01710.14120.00460.00570.12140.01070.1193-19.49040.0477-0.6288
60.8443-0.39470.22442.01911.4971.761-0.01430.0488-0.1505-0.0551-0.06250.01960.0409-0.05810.10580.1038-0.00660.00890.10230.00690.1434-25.9364-3.8328-12.1233
71.62880.6898-0.6552.16240.20642.27970.0786-0.14930.07110.2957-0.0242-0.1931-0.35720.1678-0.06060.14280.0005-0.02460.117-0.00870.1152-17.516211.074-5.2826
84.3563-3.2152-0.21495.57981.24122.92240.05190.3289-0.0623-0.2517-0.1164-0.04010.0856-0.23470.07910.1611-0.0075-0.00710.1324-0.0040.133-17.83680.7031-24.2096
91.3182-0.0083-1.39551.01630.23373.985-0.01770.0093-0.01230.0735-0.0045-0.07110.19080.05940.03980.17180.019-0.01390.15760.01030.1895-18.3394-10.2866-8.8372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 269 through 283 )
2X-RAY DIFFRACTION2chain 'A' and (resid 284 through 307 )
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 322 )
4X-RAY DIFFRACTION4chain 'A' and (resid 323 through 335 )
5X-RAY DIFFRACTION5chain 'A' and (resid 336 through 357 )
6X-RAY DIFFRACTION6chain 'A' and (resid 358 through 368 )
7X-RAY DIFFRACTION7chain 'A' and (resid 369 through 382 )
8X-RAY DIFFRACTION8chain 'A' and (resid 383 through 394 )
9X-RAY DIFFRACTION9chain 'A' and (resid 395 through 418 )

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