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- PDB-9d04: CO-CRYSTAL STRUCTURE OF CIRCULARLY PERMUTED HUMAN TASPASE-1 BOUND... -

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Basic information

Entry
Database: PDB / ID: 9d04
TitleCO-CRYSTAL STRUCTURE OF CIRCULARLY PERMUTED HUMAN TASPASE-1 BOUND TO LIGAND SMDC994967 1-(ETHENESULFONYL)-4-{[4- (TRIFLUOROMETHOXY)PHENYL]METHYL}PIPERAZINE
ComponentsThreonine aspartase subunit beta,Threonine aspartase subunit alpha
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: 2.1 Å
AuthorsDelker, S.L. / Edwards, T.E. / Abendroth, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)F32GM139242 United States
CitationJournal: TO BE PUBLISHED
Title: CO-CRYSTAL STRUCTURE OF CIRCULARLY PERMUTED HUMAN TASPASE-1 BOUND TO LIGAND SMDC994967 1-(ETHENESULFONYL)-4-{[4- (TRIFLUOROMETHOXY)PHENYL]METHYL}PIPERAZINE
Authors: Delker, S.L. / Edwards, T.E. / Abendroth, J.
History
DepositionAug 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine aspartase subunit beta,Threonine aspartase subunit alpha
B: Threonine aspartase subunit beta,Threonine aspartase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5419
Polymers70,6882
Non-polymers8537
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-53 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.280, 60.280, 318.130
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 subunit beta,Threonine aspartase subunit alpha


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: VCID 11900 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H6P5
#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.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-R1G / 1-(ethenylsulfonyl)-4-{[4-(trifluoromethoxy)phenyl]methyl}piperazine


Mass: 350.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H17F3N2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.8
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 SCREEN CONDITION B11 CONTAINING 0.1M MES, PH 5.8, 17% PEG 6000, 0.2M CALCIUM CHLORIDE + 2. ...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 SCREEN CONDITION B11 CONTAINING 0.1M MES, PH 5.8, 17% PEG 6000, 0.2M CALCIUM CHLORIDE + 2.5MM 107546 (SMDC994967) SUPPLEMENTED WITH 20% ETHYLENE GLYCOL AS A CRYO-PROTECTANT, CRYSTAL TRACKING ID 282660C3, UNIQUE PUCK ID GSA4-1

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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 MX-300 / Detector: CCD / Date: Aug 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→30.14 Å / Num. obs: 38039 / % possible obs: 99.9 % / Redundancy: 5.85 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.25
Reflection shellResolution: 2.1→30.14 Å / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 3.47 / Num. unique obs: 22245 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXDEV_2467refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal structure

Resolution: 2.1→30.14 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.71
RfactorNum. reflection% reflection
Rfree0.198 1975 5.21 %
Rwork0.153 --
obs0.156 37912 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.9 Å2 / Biso mean: 44.32 Å2 / Biso min: 16.59 Å2
Refinement stepCycle: final / Resolution: 2.1→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 51 243 4764
Biso mean--46.48 43.75 -
Num. residues----631
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.275 165 -
Rwork0.2092 2600 -
all-2765 -
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)
16.8988-2.177-2.58013.01131.69162.873-0.0642-0.08740.1577-0.04060.0772-0.0397-0.34830.1749-0.05840.2789-0.0801-0.05480.16080.05190.1773.411315.2416-9.5202
22.7528-1.21780.27974.0847-0.46235.5088-0.1765-0.3999-0.18010.1560.18060.39240.0735-0.12440.00380.2774-0.0903-0.01490.23740.04160.2422-3.39767.195-1.3985
33.4739-1.51790.66694.7661-0.49424.6499-0.0904-0.2305-0.09710.24680.04280.0431-0.07140.18340.06360.2982-0.07980.02370.29570.02210.14230.914311.12433.5029
42.4413-0.75530.57744.3991-1.41024.29-0.0684-0.29360.5360.0501-0.0553-0.1532-0.94450.44640.1270.5541-0.1276-0.03350.3462-0.09820.28033.441323.40393.3113
52.2518-0.1426-0.62592.66930.19182.37450.0021-0.06080.2119-0.22350.0805-0.242-0.54110.2162-0.07720.4409-0.1578-0.04380.20230.02150.23655.638919.5185-13.7192
66.13980.0079-0.9626.6554-0.29126.208-0.21520.53370.5063-0.59030.1296-0.3623-0.53540.17140.060.5475-0.1354-0.05980.24350.04230.21473.912117.985-24.8595
71.3764-0.82971.16267.7823-5.9857.3719-0.09780.1205-0.1681-0.49790.12080.00870.23950.0365-0.04770.2243-0.0554-0.00980.1671-0.01130.20031.3615-7.2821-21.9448
87.92722.32570.02915.21161.07952.54640.0657-0.30110.21360.2259-0.07651.0238-0.0155-0.2848-0.05080.2925-0.07310.01280.22130.00670.3992-7.4834-7.6092-11.7814
94.55871.11850.32963.9566-0.43196.72460.0068-0.46210.4740.53030.03890.9919-0.8136-0.4599-0.05010.4108-0.1120.0630.2995-0.05380.6121-11.1599-8.5498-15.042
104.34011.0717-0.36383.9190.30693.76840.0090.2411-0.1996-0.61290.02740.7080.5533-0.1626-0.03880.4787-0.1448-0.09370.2009-0.02550.523-9.3345-18.806-22.9499
111.50250.32050.17973.0438-1.61292.0623-0.09850.3055-0.3586-0.76770.0751-0.06720.31440.1718-0.00010.4084-0.05060.01170.2474-0.04550.26514.9756-11.1053-26.9921
127.8841-0.72011.0156.6609-1.06024.8266-0.03350.0621-0.3309-0.48090.0948-0.93110.02870.89930.04370.261-0.09880.06390.3175-0.01160.330816.0606-3.0251-20.796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0
2X-RAY DIFFRACTION2A0
3X-RAY DIFFRACTION3A0
4X-RAY DIFFRACTION4A0
5X-RAY DIFFRACTION5A0
6X-RAY DIFFRACTION6A0
7X-RAY DIFFRACTION7B0
8X-RAY DIFFRACTION8B0
9X-RAY DIFFRACTION9B0
10X-RAY DIFFRACTION10B0
11X-RAY DIFFRACTION11B0
12X-RAY DIFFRACTION12B0

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