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- PDB-2jii: Structure of vaccinia related kinase 3 -

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Basic information

Entry
Database: PDB / ID: 2jii
TitleStructure of vaccinia related kinase 3
ComponentsSERINE/THREONINE-PROTEIN KINASE VRK3 MOLECULE: VACCINIA RELATED KINASE 3
KeywordsTRANSFERASE / PSEUDO KINASE DOMAIN / VACCINIA RELATED KINASE / SERINE/THREONINE-PROTEIN KINASE / VRK3 / KINASE / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


ERKs are inactivated / positive regulation of phosphoprotein phosphatase activity / negative regulation of ERK1 and ERK2 cascade / peptidyl-serine phosphorylation / protein phosphatase binding / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / nucleolus / nucleoplasm / ATP binding ...ERKs are inactivated / positive regulation of phosphoprotein phosphatase activity / negative regulation of ERK1 and ERK2 cascade / peptidyl-serine phosphorylation / protein phosphatase binding / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / nucleolus / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Zinc-ribbon domain / zinc-ribbon domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain ...Zinc-ribbon domain / zinc-ribbon domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
Inactive serine/threonine-protein kinase VRK3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBunkoczi, G. / Eswaran, J. / Pike, A.C.W. / Uppenberg, J. / Ugochukwu, E. / von Delft, F. / Cooper, C. / Salah, E. / Savitsky, P. / Burgess-Brown, N. ...Bunkoczi, G. / Eswaran, J. / Pike, A.C.W. / Uppenberg, J. / Ugochukwu, E. / von Delft, F. / Cooper, C. / Salah, E. / Savitsky, P. / Burgess-Brown, N. / Keates, T. / Fedorov, O. / Sobott, 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
DepositionJun 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 1, 2024Group: 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 / 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 / _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 VRK3 MOLECULE: VACCINIA RELATED KINASE 3
B: SERINE/THREONINE-PROTEIN KINASE VRK3 MOLECULE: VACCINIA RELATED KINASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1137
Polymers79,8032
Non-polymers3105
Water9,260514
1
A: SERINE/THREONINE-PROTEIN KINASE VRK3 MOLECULE: VACCINIA RELATED KINASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0884
Polymers39,9021
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SERINE/THREONINE-PROTEIN KINASE VRK3 MOLECULE: VACCINIA RELATED KINASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0263
Polymers39,9021
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.258, 54.423, 91.822
Angle α, β, γ (deg.)90.00, 91.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 5 / Auth seq-ID: 141 - 472 / Label seq-ID: 19 - 350

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.10368, 0.01602, -0.99448), (-0.0082, 0.99982, 0.01697), (0.99458, 0.00991, -0.10353)
Vector: 141.35913, -12.82482, -39.77009)

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE VRK3 MOLECULE: VACCINIA RELATED KINASE 3


Mass: 39901.578 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 146-474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3
References: UniProt: Q8IV63, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 123-145 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH=7.5 2.0 M AMMONIUMFORMATE, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0331
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 16, 2007
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2→46.8 Å / Num. obs: 60969 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.2 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENSEMBLE

Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.389 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3092 5.1 %RANDOM
Rwork0.179 ---
obs0.181 57853 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.27 Å2
2---1.27 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5111 0 20 514 5645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225294
X-RAY DIFFRACTIONr_bond_other_d0.0010.023639
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9697181
X-RAY DIFFRACTIONr_angle_other_deg0.9338867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9755643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59124.098244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80915873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8431529
X-RAY DIFFRACTIONr_chiral_restr0.070.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021069
X-RAY DIFFRACTIONr_nbd_refined0.1950.21104
X-RAY DIFFRACTIONr_nbd_other0.1830.23734
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22530
X-RAY DIFFRACTIONr_nbtor_other0.0840.22632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2388
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.04733326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.01455227
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.36482246
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.95111954
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 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1882medium positional0.230.5
2406loose positional0.55
1882medium thermal0.812
2406loose thermal0.8810
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 237
Rwork0.271 4009
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)
10.5613-0.5987-0.12472.71090.74370.7511-0.0239-0.09830.33980.07110.1744-0.0326-0.04380.0708-0.1505-0.1003-0.001-0.0105-0.03730.01930.113266.954229.229748.379
22.9253-0.0584-0.08142.02060.07950.8504-0.0240.2177-0.23490.0240.02770.1220.0802-0.08-0.0038-0.12330.00490.0076-0.0744-0.0091-0.036659.69278.651239.775
31.01610.07790.09362.0203-0.53992.21260.00130.015-0.0188-0.03940.1156-0.0004-0.0247-0.0294-0.1168-0.06820.00260.0233-0.1115-0.0174-0.1186.51716.296721.6835
41.0816-0.2543-0.36711.76560.21351.8008-0.0081-0.00030.0686-0.01320.0561-0.10120.07020.1358-0.048-0.06130.0007-0.0091-0.1221-0.0126-0.129795.9627-4.020615.6224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A141 - 262
2X-RAY DIFFRACTION2A263 - 472
3X-RAY DIFFRACTION3B137 - 262
4X-RAY DIFFRACTION4B263 - 472

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