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- PDB-3op5: Human vaccinia-related kinase 1 -

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Basic information

Entry
Database: PDB / ID: 3op5
TitleHuman vaccinia-related kinase 1
ComponentsSerine/threonine-protein kinase VRK1
KeywordsTRANSFERASE / Adenosine Triphosphate / Amino Acid Sequence / Binding Sites / Catalytic Domain / Models / Molecular / Molecular Sequence Data / Phosphotransferases / Protein Conformation / Protein Folding / Surface Entropy Reduction / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H2AX kinase activity / Golgi disassembly / Cajal body organization / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / histone H3S10 kinase activity / regulation of neuron migration / Initiation of Nuclear Envelope (NE) Reformation ...histone H2AX kinase activity / Golgi disassembly / Cajal body organization / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / histone H3S10 kinase activity / regulation of neuron migration / Initiation of Nuclear Envelope (NE) Reformation / Golgi stack / nucleosomal DNA binding / Cajal body / neuron projection development / kinase activity / protein autophosphorylation / histone binding / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / protein kinase binding / chromatin / nucleolus / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Chem-REB / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAllerston, C.K. / Uttarkar, S. / Savitsky, P. / Elkins, J.M. / Filippakopoulos, P. / Krojer, T. / Rellos, P. / Fedorov, O. / Eswaran, J. / Brenner, B. ...Allerston, C.K. / Uttarkar, S. / Savitsky, P. / Elkins, J.M. / Filippakopoulos, P. / Krojer, T. / Rellos, P. / Fedorov, O. / Eswaran, J. / Brenner, B. / Keates, T. / Das, S. / King, O. / Chalk, R. / Berridge, G. / von Delft, F. / Gileadi, O. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Sci Rep / Year: 2017
Title: Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.
Authors: Counago, R.M. / Allerston, C.K. / Savitsky, P. / Azevedo, H. / Godoi, P.H. / Wells, C.I. / Mascarello, A. / de Souza Gama, F.H. / Massirer, K.B. / Zuercher, W.J. / Guimaraes, C.R.W. / Gileadi, O.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 29, 2012Group: Structure summary
Revision 1.3Jan 30, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 VRK1
B: Serine/threonine-protein kinase VRK1
C: Serine/threonine-protein kinase VRK1
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,37315
Polymers164,5534
Non-polymers1,82011
Water16,214900
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6244
Polymers41,1381
Non-polymers4863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6244
Polymers41,1381
Non-polymers4863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6565
Polymers41,1381
Non-polymers5184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4692
Polymers41,1381
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.970, 97.190, 191.990
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
Serine/threonine-protein kinase VRK1 / Vaccinia-related kinase 1


Mass: 41138.125 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN, RESIDUES 3-369
Mutation: K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2
References: UniProt: Q99986, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-REB / [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile


Mass: 331.374 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H17N7
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 900 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2m K/Na(tartrate), 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2010
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 6.2 / Number: 240388 / Rsym value: 0.113 / D res high: 2.4 Å / D res low: 46.338 Å / Num. obs: 67821 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.5946.3496.510.0320.0323.5
5.377.5995.910.0620.0623.4
4.385.3798.110.0640.0643.5
3.794.389910.060.063.5
3.393.7999.410.0830.0833.5
3.13.3999.610.1250.1253.6
2.873.199.310.1960.1963.6
2.682.8799.210.3050.3053.6
2.532.6899.810.4440.4443.6
2.42.5398.610.5480.5483.4
ReflectionResolution: 2.4→46.338 Å / Num. all: 67821 / Num. obs: 67821 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 47.65 Å2 / Rsym value: 0.113 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.4-2.533.40.5481.40.548198.6
2.53-2.683.60.4441.70.444199.8
2.68-2.873.60.3052.50.305199.2
2.87-3.13.60.1963.90.196199.3
3.1-3.393.60.12560.125199.6
3.39-3.793.50.0838.60.083199.4
3.79-4.383.50.0611.20.06199
4.38-5.373.50.0649.70.064198.1
5.37-7.593.40.0629.50.062195.9
7.59-46.3383.50.03216.60.032196.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
PROTEUM PLUSPLUSdata collection
MOSFLMdata reduction
PHASERphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENSEMBL OF PDB ENTRIES 2V62, 2JII and 1CKJ

2v62

2jii

1ckj


Resolution: 2.4→46.338 Å / Cor.coef. Fo:Fc: 0.9412 / Cor.coef. Fo:Fc free: 0.9127 / Occupancy max: 1 / Occupancy min: 0.05 / SU B: 7.378 / SU ML: 0.169 / SU R Cruickshank DPI: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 2007 2.96 %RANDOM
Rwork0.1783 ---
obs0.1793 67764 98.55 %-
all-65757 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.5191 Å20 Å20 Å2
2---3.5682 Å20 Å2
3---5.0873 Å2
Refine analyzeLuzzati coordinate error obs: 0.285 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9754 0 132 900 10786
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910128HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9713709HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4560SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes249HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1487HARMONIC5
X-RAY DIFFRACTIONt_it10128HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.02
X-RAY DIFFRACTIONt_other_torsion2.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1285SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12127SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2492 145 2.98 %
Rwork0.2119 4719 -
all0.213 4864 -
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)
10.5555-0.0806-0.63061.32270.70132.2426-0.0038-0.02960.07120.01510.0153-0.0751-0.1906-0.0018-0.0114-0.0650.00840.0078-0.0133-0.0085-0.154318.03591.998820.4199
21.05040.18960.83320.57310.62842.7679-0.01780.1379-0.0596-0.04010.0041-0.10740.1140.46960.0137-0.05130.0567-0.0182-0.0094-0.0029-0.182325.99161.878367.7305
32.17770.49640.13782.0421-0.15651.63910.0339-0.083-0.43760.11860.0921-0.12750.1225-0.0939-0.126-0.19140.0186-0.0135-0.1168-0.0001-0.0882-19.968710.541393.8917
41.46410.4469-0.32671.5514-0.39512.2053-0.04220.30580.0229-0.0160.13220.39070.221-0.5415-0.0901-0.1558-0.02950.0117-0.0195-0.0003-0.1693-14.90951.989553.0159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A21 - 341
2X-RAY DIFFRACTION2{ B|* }B21 - 341
3X-RAY DIFFRACTION3{ C|* }C22 - 341
4X-RAY DIFFRACTION4{ D|* }D25 - 341

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