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- PDB-7tcy: The ubiquitin-associated domain of human thirty-eight negative ki... -

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Basic information

Entry
Database: PDB / ID: 7tcy
TitleThe ubiquitin-associated domain of human thirty-eight negative kinase I
ComponentsNon-receptor tyrosine-protein kinase TNK1
KeywordsTRANSFERASE / Kinase / Ubiquitin-associated / UBA / ONCOPROTEIN
Function / homology
Function and homology information


non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / protein autophosphorylation / protein tyrosine kinase activity / protein phosphorylation / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / : / SAM domain-like / : / Src homology 3 domains / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. ...: / : / SAM domain-like / : / Src homology 3 domains / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / PHOSPHATE ION / Non-receptor tyrosine-protein kinase TNK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsNawarathnage, S. / Bunn, R.D. / Stewart, C. / Doukov, T. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Structure / Year: 2023
Title: Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain.
Authors: Nawarathnage, S. / Tseng, Y.J. / Soleimani, S. / Smith, T. / Pedroza Romo, M.J. / Abiodun, W.O. / Egbert, C.M. / Madhusanka, D. / Bunn, D. / Woods, B. / Tsubaki, E. / Stewart, C. / Brown, S. ...Authors: Nawarathnage, S. / Tseng, Y.J. / Soleimani, S. / Smith, T. / Pedroza Romo, M.J. / Abiodun, W.O. / Egbert, C.M. / Madhusanka, D. / Bunn, D. / Woods, B. / Tsubaki, E. / Stewart, C. / Brown, S. / Doukov, T. / Andersen, J.L. / Moody, J.D.
History
DepositionDec 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 20, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-receptor tyrosine-protein kinase TNK1
B: Non-receptor tyrosine-protein kinase TNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,88210
Polymers17,5082
Non-polymers3748
Water2,288127
1
A: Non-receptor tyrosine-protein kinase TNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0828
Polymers8,7541
Non-polymers3287
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-receptor tyrosine-protein kinase TNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8002
Polymers8,7541
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.734, 88.070, 26.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-851-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Non-receptor tyrosine-protein kinase TNK1 / CD38 negative kinase 1


Mass: 8753.857 Da / Num. of mol.: 2 / Fragment: UBA domain (UNP residues 589-666) / Mutation: P589G, C610A, C644A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNK1 / Plasmid: pET42_SUMO
Details (production host): Cleavable N-terminus 10X His-SUMO tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B
References: UniProt: Q13470, non-specific protein-tyrosine kinase

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Non-polymers , 5 types, 135 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.79 Å3/Da / Density % sol: 31.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 100 mM Bis-Tris, pH 6.8, 100 mM magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2021
Details: Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.54→44.03 Å / Num. obs: 19047 / % possible obs: 97.62 % / Redundancy: 10 % / Biso Wilson estimate: 21.01 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05574 / Rpim(I) all: 0.01839 / Rrim(I) all: 0.05883 / Net I/σ(I): 19.86
Reflection shellResolution: 1.54→1.595 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.8132 / Mean I/σ(I) obs: 2.48 / Num. unique obs: 1846 / CC1/2: 0.882 / CC star: 0.968 / Rpim(I) all: 0.2892 / Rrim(I) all: 0.8652 / % possible all: 99.51

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.9model building
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→44.03 Å / SU ML: 0.1917 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2137 1001 5.26 %
Rwork0.1886 18045 -
obs0.1899 19046 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.35 Å2
Refinement stepCycle: LAST / Resolution: 1.54→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 20 127 1348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011277
X-RAY DIFFRACTIONf_angle_d1.15971736
X-RAY DIFFRACTIONf_chiral_restr0.0666198
X-RAY DIFFRACTIONf_plane_restr0.0083223
X-RAY DIFFRACTIONf_dihedral_angle_d14.7171461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.620.33241330.27762571X-RAY DIFFRACTION99.67
1.62-1.720.28711420.2292588X-RAY DIFFRACTION99.74
1.72-1.850.25781540.22252567X-RAY DIFFRACTION99.71
1.85-2.040.19681162254X-RAY DIFFRACTION85.19
2.04-2.330.21881400.18372621X-RAY DIFFRACTION99.86
2.33-2.940.19031650.1722642X-RAY DIFFRACTION99.61
2.94-44.030.20571510.17862802X-RAY DIFFRACTION99.8
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)
16.0831878121-5.22834042383-4.58911091184.570225904234.004107073483.599365302490.1026620070250.179741456086-0.340428548181-0.345140148202-0.5149718466460.992552965653-0.195202305755-0.6641474176740.3879099097860.2305440186570.0258321422659-0.050616313390.2839609322120.01648724553510.2323654330515.048261197518.29021643096.67436817048
23.9484961842.648776076152.433992333486.876860510195.279759497257.97803409330.0477987708546-0.134998477713-0.0447162553024-0.04629987165390.0477788742377-0.078158917890.301767715861-0.238810632499-0.08042887625460.143535086514-0.00991520225222-0.000141868152890.1751818734130.02239890848930.11040365245122.101824524114.32164230369.90037867696
37.9921513582-5.71704893791-3.011257137219.123338272054.438624776937.06083249377-0.00939254394231-0.0971930869754-0.1482620775520.2060025531080.0385402261917-0.2692215629590.1701267274240.0633870329834-0.01422788664920.115514214994-0.0248382948629-0.01636381824770.112951264246-0.006599573597580.10283047466629.133235890911.65517547733.62559377479
49.11736338738-3.167236682426.278972817186.63127756686-2.623232773879.260667369430.154295945499-0.269894306936-0.001148146414550.120191846771-0.106599799253-0.3196776892810.226606457020.2072410330930.003917443142940.167590693426-0.01732159413920.001784647047490.188191432194-0.01128174642560.1541243937837.100735461310.6132077107-2.03880502605
55.70593062022-0.4931946498850.05256896178148.243435541210.03111363401696.239651266260.05089919315560.152853827687-0.396288917837-0.428033762889-0.0493807009369-0.06703931375760.326594488885-0.0771682194959-0.01371483138640.146657957607-0.000240554208325-0.005399900189150.138067008909-0.02883467156710.11128031508830.09932099035.64831221805-7.32323884045
65.573726040494.561903590363.947522959965.73410931725.339715786715.078903272760.029133611554-0.73646258623-0.1339040999950.9333802227580.04627131714310.01277896370810.77860969872-0.241449464499-0.05421331342510.2495429532180.04815499910070.01470431098750.3090262801720.02938328479850.17759152982617.816188961423.5563587884-4.2760864697
74.78432411686-4.20200513761-2.666541716363.819032818853.303530887266.696488074420.5930636100610.4411482205310.306233792162-0.764588888823-0.462050313315-0.00852545394917-0.660106587552-0.490959131498-0.1475851245320.2607791556480.0192224140695-0.008642118274390.202091600001-0.002067297466750.18004172135923.509100602229.6218499343-8.1622104197
87.336073461833.178619050840.9590872720992.786374403553.062610868337.814532798660.09801239448020.2869057828610.540382597394-0.570049108034-0.0636358464221-0.220702748254-0.3352657430610.0320371870755-0.03227497468580.1439297397440.009341955870890.02075153529710.1257282288360.01199665111480.15128730037729.747487079934.1474281097-2.16581080093
90.181154207063-0.368094153804-0.2809978842750.8714752039250.6627181730570.4974404953480.0963906496110.1369454791110.273224547884-0.412042705655-0.175984962368-0.335697312874-0.628481692710.508327010765-0.1520312909810.793858862974-0.405442244233-0.0398702421160.4302445099150.72338911771.0416750215736.014491613344.96408416730.021803381358
102.241019595580.3674185319050.5076607679149.24324876971-0.7876921868052.129806896-0.297683096390.3533414511760.0551782175135-0.269247404648-0.165354060128-0.8172544017520.4631985907950.3428382288610.5057380758530.1640787976210.01087521440990.01767546388480.2265681038890.01350964774880.27729072874235.850566861734.42979122784.67419876846
114.489577006053.884421089824.72075862493.809775653232.725550328459.19694437720.211926731109-0.472039442490.5524284027080.60326224491-0.1530404990070.207357056731-0.166643285947-0.818776211635-0.06967049383010.162047564210.002856555289470.0202234816590.265594298891-0.06794827304690.33970584168631.83312771442.94317415248.84662659978
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 589 through 601 )AA589 - 6011 - 13
22chain 'A' and (resid 602 through 620 )AA602 - 62014 - 32
33chain 'A' and (resid 621 through 637 )AA621 - 63733 - 49
44chain 'A' and (resid 638 through 650 )AA638 - 65050 - 62
55chain 'A' and (resid 651 through 665 )AA651 - 66563 - 77
66chain 'B' and (resid 589 through 601 )BI589 - 6011 - 13
77chain 'B' and (resid 602 through 620 )BI602 - 62014 - 32
88chain 'B' and (resid 621 through 635 )BI621 - 63533 - 47
99chain 'B' and (resid 636 through 640 )BI636 - 64048 - 52
1010chain 'B' and (resid 641 through 654 )BI641 - 65453 - 66
1111chain 'B' and (resid 655 through 665 )BI655 - 66567 - 77

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