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- PDB-6ugk: CRYSTAL STRUCTURE OF CIRCULARLY PERMUTED HUMAN TASPASE-1 -

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Basic information

Entry
Database: PDB / ID: 6ugk
TitleCRYSTAL STRUCTURE OF CIRCULARLY PERMUTED HUMAN TASPASE-1
ComponentsThreonine aspartase 1,Threonine aspartase 1
KeywordsHYDROLASE / MLL / TASPASE-1 / CIRCULAR PERMUTATION
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases / Formation of WDR5-containing histone-modifying complexes / threonine-type endopeptidase activity / protein maturation / positive regulation of DNA-templated transcription / proteolysis / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Threonine aspartase 1 / Peptidase T2, asparaginase 2 / Asparaginase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Threonine aspartase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsEdwards, T.E. / Delker, S.L.
CitationJournal: Structure / Year: 2021
Title: Structural insights into the function of the catalytically active human Taspase1.
Authors: Nagaratnam, N. / Delker, S.L. / Jernigan, R. / Edwards, T.E. / Snider, J. / Thifault, D. / Williams, D. / Nannenga, B.L. / Stofega, M. / Sambucetti, L. / Hsieh, J.J. / Flint, A.J. / Fromme, ...Authors: Nagaratnam, N. / Delker, S.L. / Jernigan, R. / Edwards, T.E. / Snider, J. / Thifault, D. / Williams, D. / Nannenga, B.L. / Stofega, M. / Sambucetti, L. / Hsieh, J.J. / Flint, A.J. / Fromme, P. / Martin-Garcia, J.M.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author / database_2
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
Revision 1.2Oct 11, 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: Threonine aspartase 1,Threonine aspartase 1
B: Threonine aspartase 1,Threonine aspartase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8768
Polymers70,6882
Non-polymers1886
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-68 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.300, 60.300, 319.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Threonine aspartase 1,Threonine aspartase 1 / Taspase-1


Mass: 35343.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TASP1, C20orf13 / Plasmid: CID 11900 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9H6P5, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: human taspase-1 VCID 11900 at 9.23 mg/mL in 20 mM HEPES pH 8, 0.5 M NaCl, 5% glycerol against PACT B11 optimization screen containing 16% PEG 6000, 0.1 M MES pH 5.8, 0.2 M calcium chloride ...Details: human taspase-1 VCID 11900 at 9.23 mg/mL in 20 mM HEPES pH 8, 0.5 M NaCl, 5% glycerol against PACT B11 optimization screen containing 16% PEG 6000, 0.1 M MES pH 5.8, 0.2 M calcium chloride supplemented with 20% ethylene glycol as a cryo-protectant, crystal tracking ID 271056c2, unique puck ID izc9-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→40.41 Å / Num. obs: 35513 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 39.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.086 / Χ2: 0.966 / Net I/σ(I): 15.24 / Num. measured all: 206406
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.74 / Num. measured obs: 2167 / Num. possible: 429 / Num. unique obs: 412 / CC1/2: 0.997 / Rrim(I) all: 0.044 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXDEV_2328refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A8J

2a8j


Resolution: 2.15→40.41 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 1709 4.83 %
Rwork0.159 --
obs0.161 35417 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.32 Å2 / Biso mean: 43.48 Å2 / Biso min: 18.07 Å2
Refinement stepCycle: final / Resolution: 2.15→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4353 0 6 183 4542
Biso mean--42.79 43.9 -
Num. residues----620
LS refinement shellResolution: 2.15→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2361 156 -
Rwork0.1889 2762 -
all-2918 -
obs--100 %
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)
18.1618-1.8754-2.06831.82361.30922.5181-0.1233-0.16120.01240.01220.0695-0.0188-0.21280.02080.08250.3161-0.0989-0.06740.16890.0840.1681-1.065412.8501-8.3558
23.221-2.02870.344.7913-0.22042.6997-0.1618-0.4247-0.29850.27890.18520.30180.0618-0.006-0.02230.2758-0.083-0.00640.28560.05210.1711-0.89457.52852.0359
33.853-3.04562.09277.6499-3.24423.8173-0.28-0.41770.38310.48190.1298-0.2223-0.7390.42390.18620.4017-0.1228-0.03650.4226-0.0830.21286.780218.25397.4709
42.0589-0.4396-0.95155.8944-1.60564.41520.044-0.17870.54550.0173-0.1242-0.2493-1.10380.77760.07910.6565-0.1436-0.05240.3096-0.07320.29222.44225.52180.4077
52.55610.7023-0.38062.29860.18031.54460.0309-0.03360.2605-0.18230.0333-0.1681-0.58490.2302-0.05520.4989-0.1876-0.06390.20870.03470.2585.884219.1912-13.9289
61.3003-1.334-1.02095.81590.17073.8055-0.02290.25070.3145-0.39130.0109-0.3448-0.53430.1716-0.01010.602-0.1745-0.07580.28960.04060.24043.625718.0478-24.8302
71.4116-0.22860.42954.2655-1.70662.5243-0.0398-0.0066-0.14970.0770.22480.4929-0.0202-0.0752-0.19460.2885-0.0971-0.02620.20690.03150.2803-1.3038-6.8207-16.6384
82.65680.29780.23393.3140.68613.9482-0.04910.007-0.1925-0.1658-0.00690.84110.298-0.25250.06190.3789-0.1564-0.06110.21970.04030.543-10.3408-15.7059-18.9808
91.74240.447-0.22313.5062-0.99082.4292-0.07080.218-0.3281-0.5470.0507-0.19990.14860.40350.010.3126-0.04270.0230.2472-0.01820.2368.583-8.6015-24.9831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 2:52A2 - 52
2X-RAY DIFFRACTION2chain A and resid 53:174A53 - 174
3X-RAY DIFFRACTION3chain A and resid 175:226A175 - 226
4X-RAY DIFFRACTION4chain A and resid 227:286A227 - 286
5X-RAY DIFFRACTION5chain A and resid 287:338A287 - 338
6X-RAY DIFFRACTION6chain B and resid 2:52B2 - 52
7X-RAY DIFFRACTION7chain B and resid 53:225B53 - 225
8X-RAY DIFFRACTION8chain B and resid 226:298B226 - 298
9X-RAY DIFFRACTION9chain B and resid 299:330B299 - 330

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