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- PDB-9d02: Co-crystal structure of circularly permuted human taspase-1 bound... -

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Basic information

Entry
Database: PDB / ID: 9d02
TitleCo-crystal structure of circularly permuted human taspase-1 bound to ligand SMDC1014883 (2R)-4-(ethenesulfonyl)-1-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}-2-[(prop-2-yn-1-yloxy)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: 2.15 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)71,6788
Polymers70,6882
Non-polymers9906
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-41 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.430, 60.430, 317.710
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-R1J / (2R)-4-(ethenylsulfonyl)-1-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}-2-{[(prop-2-yn-1-yl)oxy]methyl}piperazine


Mass: 436.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20F4N2O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 287 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 108131 (SMDC1014883) supplemented with 20% ethylene glycol as a cryo-protectant, crystal tracking ID 291536 B3, unique puck ID zhg3-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→49.71 Å / Num. obs: 35557 / % possible obs: 99.9 % / Redundancy: 5.699 % / Biso Wilson estimate: 45.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.081 / Χ2: 0.988 / Net I/σ(I): 15.07 / Num. measured all: 202637
Reflection shellResolution: 2.15→49.71 Å / Redundancy: 5.334 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.91 / Num. measured obs: 2251 / Num. possible: 430 / Num. unique obs: 422 / CC1/2: 0.997 / Rrim(I) all: 0.048 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXDEV_2733refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal molecule

Resolution: 2.15→49.71 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.03
RfactorNum. reflection% reflection
Rfree0.195 1964 5.54 %
Rwork0.157 --
obs0.159 35442 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.32 Å2 / Biso mean: 52.42 Å2 / Biso min: 18.25 Å2
Refinement stepCycle: final / Resolution: 2.15→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 62 156 4684
Biso mean--53.03 47.87 -
Num. residues----629
LS refinement shellResolution: 2.15→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2917 147 -
Rwork0.2296 2332 -
all-2479 -
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)
16.1265-0.745-1.99352.67161.82093.385-0.1129-0.21810.0325-0.10580.11690.0929-0.43790.23630.00890.3766-0.0839-0.04940.2240.07160.20983.341915.5437-9.5669
23.9923-1.43560.02475.52140.31936.9847-0.1837-0.3851-0.17370.20560.26570.3090.24590.0314-0.07960.3115-0.08050.00340.27110.04980.2394-2.15157.2938-0.4945
31.81120.1782-0.74322.12230.04733.068-0.0406-0.32660.37980.02530.0948-0.0431-0.80290.3692-0.04660.5154-0.1227-0.02740.3076-0.04780.30943.832121.2922-3.0016
45.5609-1.3949-2.07489.4222-0.8788.2763-0.11770.48590.3642-0.66760.0407-0.4307-0.75340.15680.05430.6556-0.16-0.07380.30420.04630.23923.194118.3251-24.7336
52.1002-0.86421.1156.8513-2.71844.3512-0.0767-0.0282-0.30190.06750.06710.16320.04290.0626-0.02250.2168-0.0735-0.0030.2270.0050.23770.268-7.4022-16.8538
66.15170.00482.52732.12163.83038.0598-0.30150.50220.3365-1.25960.25481.4315-0.9953-0.18280.00630.5595-0.1456-0.05490.39320.03480.649-6.2308-2.848-18.1627
73.570.4268-0.02424.2273-0.53774.2540.0212-0.0892-0.2080.06360.10381.30010.1248-0.3754-0.11640.3718-0.1375-0.02230.28820.06940.7293-11.7668-13.5588-17.3213
86.16271.34220.06625.25651.6365.1193-0.16950.0391-0.5397-0.36880.29750.67430.45170.0432-0.15140.5084-0.0792-0.02480.1563-0.0330.5636-6.7058-19.2999-22.7236
98.5343-2.17754.26327.7113-0.82248.13770.08280.999-0.5509-1.67130.0979-0.01250.880.3608-0.15370.7157-0.08860.02740.2933-0.08960.48311.4249-21.374-29.3441
102.0427-0.12360.40424.3203-1.38751.719-0.01450.3874-0.2406-0.6161-0.028-0.04460.15490.19980.05340.3775-0.04420.02170.2855-0.03630.24546.0023-6.9367-26.1278
114.3762-0.7375-0.73912.4162-0.46298.82240.05870.0456-0.4775-0.37740.0611-0.7160.11841.16690.05910.345-0.08060.0520.3863-0.00670.441515.9939-2.8078-21.153
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 DIFFRACTION5B0
6X-RAY DIFFRACTION6B0
7X-RAY DIFFRACTION7B0
8X-RAY DIFFRACTION8B0
9X-RAY DIFFRACTION9B0
10X-RAY DIFFRACTION10B0
11X-RAY DIFFRACTION11B0

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