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- PDB-2v62: Structure of vaccinia-related kinase 2 -

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Basic information

Entry
Database: PDB / ID: 2v62
TitleStructure of vaccinia-related kinase 2
ComponentsSERINE/THREONINE-PROTEIN KINASE VRK2
KeywordsTRANSFERASE / ATP-BINDING / MEMBRANE / NUCLEOTIDE-BINDING / TRANSMEMBRANE
Function / homology
Function and homology information


regulation of interleukin-1-mediated signaling pathway / Nuclear Envelope Breakdown / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / regulation of MAPK cascade / RHOG GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / mitochondrial membrane ...regulation of interleukin-1-mediated signaling pathway / Nuclear Envelope Breakdown / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / regulation of MAPK cascade / RHOG GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / mitochondrial membrane / nuclear envelope / cellular response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein kinase binding / endoplasmic reticulum / signal transduction / protein-containing complex / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 domain profile. / Protein kinase domain ...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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SUCCINIC ACID / Serine/threonine-protein kinase VRK2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBunkoczi, G. / Eswaran, J. / Cooper, C. / Fedorov, O. / Keates, T. / Rellos, P. / Salah, E. / Savitsky, P. / Ugochukwu, E. / von Delft, F. ...Bunkoczi, G. / Eswaran, J. / Cooper, C. / Fedorov, O. / Keates, T. / Rellos, P. / Salah, E. / Savitsky, P. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Knapp, S.
CitationJournal: Structure / Year: 2009
Title: Structure of the Pseudokinase Vrk3 Reveals a Degraded Catalytic Site, a Highly Conserved Kinase Fold, and a Putative Regulatory Binding Site.
Authors: Scheeff, E.D. / Eswaran, J. / Bunkoczi, G. / Knapp, S. / Manning, G.
History
DepositionJul 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 30, 2011Group: Derived calculations
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE VRK2
B: SERINE/THREONINE-PROTEIN KINASE VRK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8487
Polymers78,5202
Non-polymers3295
Water6,017334
1
A: SERINE/THREONINE-PROTEIN KINASE VRK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5265
Polymers39,2601
Non-polymers2674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE/THREONINE-PROTEIN KINASE VRK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3222
Polymers39,2601
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.655, 157.532, 56.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHEVALVAL5AA15 - 6225 - 72
211PHEPHEVALVAL5BB15 - 6225 - 72
121LEULEUGLUGLU3AA98 - 122108 - 132
221LEULEUGLUGLU3BB98 - 122108 - 132
112GLYGLYTYRTYR5AA68 - 9778 - 107
212GLYGLYTYRTYR5BB68 - 9778 - 107
113ARGARGGLNGLN3AA123 - 330133 - 340
213ARGARGGLNGLN3BB123 - 330133 - 340

NCS ensembles :
ID
1
2
3

NCS oper: (Code: given
Matrix: (-0.99929, 0.03772, -0.00127), (-0.03772, -0.99927, 0.00605), (-0.00104, 0.0061, 0.99998)
Vector: 35.71097, 78.92622, 27.94197)

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE VRK2 / VACCINIA RELATED PROTEIN KINASE 2


Mass: 39259.891 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 14-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: Q86Y07, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 23 RESIDUES BELONG TO AN UNCLEAVED HIS-TAG

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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 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 M SUCCINIC ACID PH=7.0 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2007
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.7→45.8 Å / Num. obs: 67759 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JII

2jii


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.559 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3413 5 %RANDOM
Rwork0.201 ---
obs0.203 64302 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.83 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 21 334 5111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224958
X-RAY DIFFRACTIONr_bond_other_d0.0020.023322
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9696727
X-RAY DIFFRACTIONr_angle_other_deg1.01238122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46924.512215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31115801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6911520
X-RAY DIFFRACTIONr_chiral_restr0.090.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025519
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02975
X-RAY DIFFRACTIONr_nbd_refined0.1980.21029
X-RAY DIFFRACTIONr_nbd_other0.1910.23320
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22372
X-RAY DIFFRACTIONr_nbtor_other0.0860.22510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.32633193
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.5954955
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.11482047
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.803111772
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1145tight positional0.040.05
31220tight positional0.030.05
1245medium positional0.040.5
2178medium positional0.120.5
1419loose positional0.035
2238loose positional0.35
31465loose positional0.055
1145tight thermal0.190.5
31220tight thermal0.270.5
1245medium thermal0.172
2178medium thermal1.072
1419loose thermal0.1810
2238loose thermal1.0610
31465loose thermal0.2410
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 217
Rwork0.312 4358
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)
13.757-2.65050.97595.7041-0.5671.69240.32180.4531-0.3997-0.9798-0.1401-0.11180.57390.4571-0.18160.28110.047-0.03880.1399-0.05120.050918.4035-1.771428.8268
24.7695-2.22051.07021.5859-0.66094.3243-0.0336-0.0893-0.53110.0180.13980.25680.3398-0.3091-0.1062-0.0869-0.0594-0.0206-0.16370.0209-0.06278.781811.672635.4781
31.0556-0.07930.13241.3213-0.42391.48930.0460.18330.159-0.1844-0.0333-0.01630.07760.021-0.0128-0.13580.00470.0018-0.12620.035-0.121316.983527.715730.1806
43.8714-2.2242-0.95525.69880.40260.94820.32590.4610.3237-1.0514-0.21040.1798-0.557-0.3261-0.11540.3050.04420.02310.12160.0460.057816.929980.031756.4216
56.447-1.5562-0.79460.58660.99333.14320.136-0.06880.5786-0.11980.0371-0.1839-0.29660.352-0.1731-0.0675-0.0690.0254-0.14250.0046-0.010827.754766.792463.5871
61.1754-0.1653-0.09481.40950.48851.67160.03510.172-0.143-0.1881-0.0208-0.039-0.10220.0361-0.0143-0.1289-0.00190.0096-0.1367-0.0179-0.100419.843650.888758.355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 67
2X-RAY DIFFRACTION1A98 - 122
3X-RAY DIFFRACTION2A68 - 97
4X-RAY DIFFRACTION3A123 - 330
5X-RAY DIFFRACTION4B1 - 67
6X-RAY DIFFRACTION4B98 - 122
7X-RAY DIFFRACTION5B68 - 97
8X-RAY DIFFRACTION6B123 - 330

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