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- PDB-5l2q: Serine/threonine-protein kinase 40 (STK40) kinase homology domain -

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Basic information

Entry
Database: PDB / ID: 5l2q
TitleSerine/threonine-protein kinase 40 (STK40) kinase homology domain
ComponentsSerine/threonine-protein kinase 40
KeywordsTRANSFERASE / pseudokinase SINK-homologous serine/threonine-protein kinase Sugen kinase 495
Function / homology
Function and homology information


respiratory system process / lung alveolus development / glycogen metabolic process / lung morphogenesis / regulation of MAPK cascade / multicellular organism growth / regulation of gene expression / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity ...respiratory system process / lung alveolus development / glycogen metabolic process / lung morphogenesis / regulation of MAPK cascade / multicellular organism growth / regulation of gene expression / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Serine/threonine-protein kinase 40 / Pseudokinase tribbles family/serine-threonine-protein kinase 40 / 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 domain profile. / Protein kinase domain ...Serine/threonine-protein kinase 40 / Pseudokinase tribbles family/serine-threonine-protein kinase 40 / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase 40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsDurzynska, I. / Uljon, S. / Blacklow, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA092443 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)K08 CA092433 United States
CitationJournal: Structure / Year: 2017
Title: STK40 Is a Pseudokinase that Binds the E3 Ubiquitin Ligase COP1.
Authors: Durzynska, I. / Xu, X. / Adelmant, G. / Ficarro, S.B. / Marto, J.A. / Sliz, P. / Uljon, S. / Blacklow, S.C.
History
DepositionAug 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Serine/threonine-protein kinase 40
B: Serine/threonine-protein kinase 40
A: Serine/threonine-protein kinase 40
D: Serine/threonine-protein kinase 40


Theoretical massNumber of molelcules
Total (without water)144,6034
Polymers144,6034
Non-polymers00
Water1,18966
1
A: Serine/threonine-protein kinase 40


Theoretical massNumber of molelcules
Total (without water)36,1511
Polymers36,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase 40


Theoretical massNumber of molelcules
Total (without water)36,1511
Polymers36,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase 40


Theoretical massNumber of molelcules
Total (without water)36,1511
Polymers36,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase 40


Theoretical massNumber of molelcules
Total (without water)36,1511
Polymers36,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.550, 237.650, 55.610
Angle α, β, γ (deg.)90.00, 106.32, 90.00
Int Tables number4
Space group name H-MP1211
DetailsElutes at expected monomer mass on SD200 size exclusion chromatography

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Components

#1: Protein
Serine/threonine-protein kinase 40 / SINK-homologous serine/threonine-protein kinase / Sugen kinase 495 / SgK495


Mass: 36150.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK40, SGK495, SHIK / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8N2I9, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.4449.51plate
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop7.5100mM Tris-HCL 7.5 21% PEG 4000 6% Glycerol 5% Tert-butanol 200mM NaCl 1mM TCEP
2932vapor diffusion, hanging drop7.5100mM Tris-HCL 7.5 18% PEG 4000 9% Tert-butanol 75mM NaCl 1mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.53→59.41 Å / Num. obs: 45250 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.52
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.49 / CC1/2: 0.6 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VZ6

2vz6


Resolution: 2.53→59.413 Å / Cross valid method: FREE R-VALUE / σ(F): 40.16 / Phase error: 38.21 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2795 2407 5.32 %
Rwork0.2576 --
obs0.2587 45250 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.53→59.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8279 0 0 66 8345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038437
X-RAY DIFFRACTIONf_angle_d0.63211524
X-RAY DIFFRACTIONf_dihedral_angle_d7.8075409
X-RAY DIFFRACTIONf_chiral_restr0.0431401
X-RAY DIFFRACTIONf_plane_restr0.0051481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5304-2.58210.39171180.38962498X-RAY DIFFRACTION95
2.5821-2.63820.37741400.3742596X-RAY DIFFRACTION94
2.6382-2.69960.41971420.36422498X-RAY DIFFRACTION94
2.6996-2.76710.36071420.35672570X-RAY DIFFRACTION94
2.7671-2.84190.36731420.36352430X-RAY DIFFRACTION93
2.8419-2.92550.38441300.34462630X-RAY DIFFRACTION95
2.9255-3.01990.39441060.33472522X-RAY DIFFRACTION95
3.0199-3.12780.36811390.32872559X-RAY DIFFRACTION94
3.1278-3.2530.33671830.32312474X-RAY DIFFRACTION92
3.253-3.4010.32571430.29972484X-RAY DIFFRACTION93
3.401-3.58020.30871330.28052494X-RAY DIFFRACTION93
3.5802-3.80440.2911480.27052508X-RAY DIFFRACTION93
3.8044-4.0980.24911370.24132534X-RAY DIFFRACTION93
4.098-4.510.23461100.20562501X-RAY DIFFRACTION93
4.51-5.16180.22191570.20732514X-RAY DIFFRACTION92
5.1618-6.50.27721590.2482497X-RAY DIFFRACTION93
6.5-44.23540.2221540.19412532X-RAY DIFFRACTION92
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)
11.0802-0.97070.35951.306-0.46580.74680.1507-0.8378-1.44710.23320.40050.3809-0.0599-0.4633-0.22470.77140.3261-0.02360.77221.51712.0009178.8938-49.400871.7276
20.0736-0.0040.21525.4994-0.70432.92270.123-0.6576-1.1640.76260.34660.0177-0.5517-0.4197-0.45880.870.27610.11681.0620.82872.0597189.85-46.196475.9239
33.66074.1432-0.11254.6928-0.253.58990.3024-0.8555-1.487-0.30240.29110.1403-0.7821-0.1514-0.35351.2216-0.00030.14170.73930.53011.0885198.0892-38.366866.804
42.5511.8318-0.11824.7303-1.23920.3153-1.1691.5227-0.518-1.2611.3316-1.5791-0.32750.1254-0.05890.989-0.43080.29331.0342-0.39431.0205162.606742.796248.3841
55.92674.26270.99415.78842.26013.45430.5523-1.44880.60430.5972-0.67920.61030.0418-0.48070.21230.5473-0.15280.12530.6709-0.19430.5858145.227841.331267.645
62.7422-0.2775-0.11463.2488-0.2564.47280.4822-1.50650.10.9411-0.60660.45050.4922-0.30750.15780.574-0.17690.17490.7077-0.43361.4701158.286410.320154.5202
74.12810.9893-0.04474.30271.1472.1422-0.1237-0.58650.60970-0.21330.4473-0.11630.04630.17120.3751-0.00350.0150.3631-0.16250.7761172.22116.136445.3782
85.232-0.06880.76235.8199-0.82526.3108-0.2216-0.02930.2187-0.02640.0067-0.5703-0.13241.21020.11170.3012-0.04850.10040.4688-0.1170.8921189.179418.247941.7866
90.43340.4919-1.69333.7881-2.32476.64660.4864-0.25370.90530.8459-0.43340.0283-0.51790.3596-0.13810.4825-0.0255-0.03610.4551-0.07891.3475174.8672-7.306453.1157
104.13950.169-0.27113.2808-0.96432.9664-0.3417-0.2637-0.23060.0121-0.0163-0.24450.2902-0.01570.18410.34490.05530.12390.17910.00680.7226164.2571-18.051346.9689
114.78230.2088-1.03774.3113-0.77635.6102-0.30070.0416-0.6246-0.15960.15290.68960.2098-0.99020.21250.3743-0.14010.05360.4218-0.07710.933142.617-21.908445.2547
129.72980.82751.25695.18124.02077.27830.30480.1305-1.1554-0.4095-0.17010.320.46340.1735-0.06191.2274-0.09450.17420.4964-0.06361.6579169.2443-52.461442.4117
131.11341.37560.87314.81271.18512.14790.24930.3585-0.7786-0.00010.5982-0.65860.46060.4437-0.41151.0944-0.24170.1679-0.10630.02042.445171.1819-48.764140.9304
140.80351.11750.26443.47910.38760.83980.0175-0.0939-0.60740.14860.09160.3048-0.0761-0.127-0.02720.7845-0.00790.11570.37440.23811.3324172.1066-38.569151.4018
151.50990.42971.66682.13930.8161.9101-0.1157-0.3133-0.1165-0.03450.3191.4007-0.3377-0.1986-0.34410.9380.02760.17870.60030.42071.9661151.5604-55.740139.7574
164.2989-0.92711.62452.3411-0.51061.89950.3019-0.3045-1.553-0.33680.11320.28620.4201-0.0418-0.12721.01680.02480.29790.51160.07461.5652182.9572-52.088450.0306
171.8491-0.58620.31112.6987-0.40461.4478-0.4239-0.604-0.9037-0.02510.5685-0.055-0.1845-0.1341-0.03150.813-0.00020.27910.55010.42021.4434182.5123-41.003760.1939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 235 through 288 )
2X-RAY DIFFRACTION2chain 'D' and (resid 289 through 320 )
3X-RAY DIFFRACTION3chain 'D' and (resid 321 through 336 )
4X-RAY DIFFRACTION4chain 'C' and (resid 37 through 151 )
5X-RAY DIFFRACTION5chain 'C' and (resid 152 through 335 )
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 100 )
7X-RAY DIFFRACTION7chain 'B' and (resid 101 through 269 )
8X-RAY DIFFRACTION8chain 'B' and (resid 270 through 336 )
9X-RAY DIFFRACTION9chain 'A' and (resid 26 through 48 )
10X-RAY DIFFRACTION10chain 'A' and (resid 49 through 229 )
11X-RAY DIFFRACTION11chain 'A' and (resid 230 through 336 )
12X-RAY DIFFRACTION12chain 'D' and (resid 30 through 48 )
13X-RAY DIFFRACTION13chain 'D' and (resid 49 through 83 )
14X-RAY DIFFRACTION14chain 'D' and (resid 84 through 111 )
15X-RAY DIFFRACTION15chain 'D' and (resid 112 through 134 )
16X-RAY DIFFRACTION16chain 'D' and (resid 135 through 170 )
17X-RAY DIFFRACTION17chain 'D' and (resid 171 through 234 )

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