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- PDB-3mtl: Crystal structure of the PCTAIRE1 kinase in complex with Indirubi... -

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Basic information

Entry
Database: PDB / ID: 3mtl
TitleCrystal structure of the PCTAIRE1 kinase in complex with Indirubin E804
ComponentsCell division protein kinase 16
KeywordsTRANSFERASE / PCTAIRE1 / kinase / Indirubin / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / growth hormone secretion / regulation of insulin secretion involved in cellular response to glucose stimulus / exocytosis / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / positive regulation of autophagy / cytoplasmic side of plasma membrane / neuron projection development ...: / growth hormone secretion / regulation of insulin secretion involved in cellular response to glucose stimulus / exocytosis / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / positive regulation of autophagy / cytoplasmic side of plasma membrane / neuron projection development / microtubule cytoskeleton / synaptic vesicle / spermatogenesis / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Haspin like 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, ATP binding site ...Haspin like 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, 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-FEF / Cyclin-dependent kinase 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKrojer, T. / Sharpe, T.D. / Roos, A. / Savitsky, P. / Amos, A. / Ayinampudi, V. / Berridge, G. / Fedorov, O. / Keates, T. / Phillips, C. ...Krojer, T. / Sharpe, T.D. / Roos, A. / Savitsky, P. / Amos, A. / Ayinampudi, V. / Berridge, G. / Fedorov, O. / Keates, T. / Phillips, C. / Burgess-Brown, N. / Zhang, Y. / Pike, A.C.W. / Muniz, J. / Vollmar, M. / Thangaratnarajah, C. / Rellos, P. / Ugochukwu, E. / Filippakopoulos, P. / Yue, W. / Das, S. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Knapp, S. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem.J. / Year: 2017
Title: Structure and inhibitor specificity of the PCTAIRE-family kinase CDK16.
Authors: Dixon-Clarke, S.E. / Shehata, S.N. / Krojer, T. / Sharpe, T.D. / von Delft, F. / Sakamoto, K. / Bullock, A.N.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein kinase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6742
Polymers37,3091
Non-polymers3651
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cell division protein kinase 16
hetero molecules

A: Cell division protein kinase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3484
Polymers74,6182
Non-polymers7312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1960 Å2
ΔGint-14 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.390, 47.390, 341.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cell division protein kinase 16 / / Serine/threonine-protein kinase PCTAIRE-1 / PCTAIRE-motif protein kinase 1


Mass: 37308.789 Da / Num. of mol.: 1 / Fragment: residues in UNP 163-478 / Mutation: S319D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / References: UniProt: Q00536, cyclin-dependent kinase
#2: Chemical ChemComp-FEF / (2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME}


Mass: 365.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N3O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 2.1M Na-formate, 0.1M Bis-Tris, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→20.09 Å / Num. all: 16459 / Num. obs: 16459 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 51.99 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 9.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2304 / Rsym value: 0.684 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UNL

1unl


Resolution: 2.4→20.09 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9214 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 1020 6.24 %RANDOM
Rwork0.1938 ---
all0.1979 16358 --
obs0.1979 16358 99.8 %-
Displacement parametersBiso max: 180.09 Å2 / Biso mean: 72.49 Å2 / Biso min: 27.76 Å2
Baniso -1Baniso -2Baniso -3
1--7.7231 Å20 Å20 Å2
2---7.7231 Å20 Å2
3---15.4463 Å2
Refine analyzeLuzzati coordinate error obs: 0.415 Å
Refinement stepCycle: LAST / Resolution: 2.4→20.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 27 101 2405
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d7832
X-RAY DIFFRACTIONt_trig_c_planes552
X-RAY DIFFRACTIONt_gen_planes3415
X-RAY DIFFRACTIONt_it233720
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3175
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_contact25824
X-RAY DIFFRACTIONt_bond_d236720.01
X-RAY DIFFRACTIONt_angle_deg322221.21
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion22.38
LS refinement shellResolution: 2.4→2.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2796 186 6.52 %
Rwork0.2147 2668 -
all0.2187 2854 -
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)
12.65662.91040.2453.5671-1.73726.90170.02190.2134-0.3763-0.03880.23360.14980.4771-0.1096-0.25550.304-0.152-0.02730.0513-0.152-0.304-12.0931-32.01588.2038
22.9095-2.90152.87263.9921-1.54738.1358-0.05550.0583-0.01480.3347-0.07470.21090.03420.07980.13010.0109-0.1520.08730.3040.0048-0.304-21.2214-17.72555.6834
33.75861.06012.31961.65250.67126.4171-0.06780.4088-0.2375-0.03550.2599-0.17240.51960.5442-0.19210.1204-0.0870.08790.2634-0.1343-0.2893-4.0764-21.153715.1762
46.9444-0.13990.4651.1425-1.07298.3155-0.1190.4660.13010.04880.3211-0.0250.0212-0.0816-0.20210.2072-0.1520.02880.2427-0.084-0.304-7.9367-14.048615.246
51.44641.0356-2.07871.65690.27297.6942-0.0197-0.19520.33660.02770.32020.2146-0.5432-0.2268-0.30060.0388-0.06930.06480.1337-0.0207-0.304-12.256-8.87331.9515
60.2054-0.4386-0.237100.25321.2381-0.0028-0.0210.0265-0.0189-0.01920.0036-0.08960.08210.0220.20230.00140.152-0.136-0.1505-0.0834-12.1823.643840.0803
72.4082-2.404-2.78024.40371.83895.4666-0.0117-0.04140.32610.04570.03410.0267-0.2026-0.0288-0.02240.29810.00990.12470.0727-0.0759-0.304-17.86552.224340.7454
80.37770.04652.79833.8689-0.42032.7222-0.00750.02130.08220.03060.07920.0658-0.06610.0143-0.07170.1405-0.152-0.0180.293-0.1148-0.3044.0582-8.338137.2782
902.66960.27912.7022-1.69684.1436-0.07070.12390.45090.18990.25240.0602-0.51020.5434-0.18170.2098-0.1520.04410.1618-0.0676-0.3040.2489-1.520725.0601
104.3784-0.0785-2.91041.6203-2.59818.1972-0.09330.24440.2126-0.01130.0179-0.2879-0.08080.21060.0754-0.1313-0.1520.0610.304-0.0975-0.3049.8598-12.629812.3446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1A 162 A 1940
2X-RAY DIFFRACTION2A 195 A 2180
3X-RAY DIFFRACTION3A 219 A 2710
4X-RAY DIFFRACTION4A 272 A 3240
5X-RAY DIFFRACTION5A 325 A 3770
6X-RAY DIFFRACTION6A 378 A 3830
7X-RAY DIFFRACTION7A 384 A 4050
8X-RAY DIFFRACTION8A 406 A 4170
9X-RAY DIFFRACTION9A 418 A 4500
10X-RAY DIFFRACTION10A 451 A 4730

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