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- PDB-9d03: Co-crystal structure of circularly permuted human taspase-1 bound... -

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Basic information

Entry
Database: PDB / ID: 9d03
TitleCo-crystal structure of circularly permuted human taspase-1 bound to ligand SMDC1014689 1-(ethenesulfonyl)-4-{[3-fluoro-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: 2.45 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 SMDC1014689 1-(ethenesulfonyl)-4-{[3-fluoro-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)71,5779
Polymers70,6882
Non-polymers8897
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-44 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.330, 60.330, 316.670
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-R1M / 1-(ethenylsulfonyl)-4-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}piperazine


Mass: 368.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16F4N2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
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 107873 (SMDC1014689) SUPPLEMENTED WITH 20% ETHYLENE GLYCOL AS A CRYO-PROTECTANT, CRYSTAL TRACKING ID 286834 A5, UNIQUE PUCK ID KJB2-3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 13, 2017
Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.45→46.83 Å / Num. obs: 23935 / % possible obs: 99.9 % / Redundancy: 7.72 % / Biso Wilson estimate: 51.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.074 / Rsym value: 0.074 / Χ2: 1.014 / Net I/σ(I): 20.95 / Num. measured all: 184707
Reflection shellResolution: 2.45→46.83 Å / Redundancy: 7.69 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 4 / Num. measured obs: 1998 / Num. possible: 298 / Num. unique obs: 283 / CC1/2: 0.999 / Rrim(I) all: 0.036 / Rsym value: 0.619 / % possible all: 100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXDEV_2621refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→46.83 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 1954 8.2 %
Rwork0.159 --
obs0.162 23829 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.86 Å2 / Biso mean: 55.22 Å2 / Biso min: 23.27 Å2
Refinement stepCycle: final / Resolution: 2.45→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4315 0 53 63 4431
Biso mean--44.38 47.14 -
Num. residues----621
LS refinement shellResolution: 2.45→2.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2558 178 -
Rwork0.2054 1561 -
all-1739 -
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)
18.35412.76112.41472.35611.77292.4972-0.12520.0312-0.0406-0.01870.09030.07360.1737-0.0250.0710.39790.11360.05840.27540.08480.227829.103638.19038.219
24.2670.715-1.79858.99053.46968.5199-0.17270.09160.2228-0.16770.6309-1.0967-0.35391.5961-0.62640.52460.0178-0.01880.53030.02930.337534.134844.13084.8157
35.56671.3232-0.98293.4921-0.37495.05-0.20610.63330.1839-0.32360.17550.08120.18970.28220.02270.41130.0342-0.04030.45110.01150.201830.869438.5729-5.3277
43.1536-0.06481.57162.06270.82243.12590.03680.2684-0.42170.12640.1417-0.24920.78990.4338-0.14950.57810.15680.05650.31930.03730.373735.829329.1278.8105
54.79571.9131.09448.67321.21748.0901-0.0859-0.724-0.20940.790.0988-0.41740.86190.1682-0.0450.64970.18310.03130.33210.01810.290533.552232.948124.6413
61.78381.4209-1.118.9311-4.99296.5512-0.07840.03520.265-0.2539-0.02120.08870.17870.05860.04970.24940.10290.02470.27330.01120.346230.527658.651516.764
78.2482-2.9199-0.9632.09223.368.6764-0.4686-0.588-0.64550.66220.07280.82381.1204-0.15760.37190.54350.15560.04970.35160.06090.52323.137454.417418.1723
86.6841-3.90050.03413.9729-2.29043.2019-0.13610.53840.1347-0.40070.17561.65040.2808-0.6394-0.00270.45550.0415-0.1130.4112-0.00620.852316.95259.99510.9795
93.27070.3033-0.39744.4491-0.7074.969-0.0571-0.08020.57770.24920.2030.9074-0.389-0.3938-0.16640.46660.15210.07550.30290.04570.759119.117368.416820.238
105.59851.5159-1.32346.2917-1.42866.22890.0801-0.42380.25551.54970.08390.1993-0.7847-0.0442-0.21570.69660.1350.04330.3066-0.15690.66528.816670.88727.4726
112.179-0.4318-0.24716.4765-2.58453.33840.0222-0.38030.42680.5914-0.0597-0.2894-0.1880.28150.05950.34870.0524-0.05970.3411-0.07520.312537.417258.276424.8375
127.79434.26522.61915.85412.26732.13190.2163-0.10240.6770.31420.0706-0.7305-0.07070.5918-0.23980.40440.1725-0.02660.4821-0.04270.45946.689452.051122.1395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-ID
1X-RAY DIFFRACTION1A
2X-RAY DIFFRACTION2A
3X-RAY DIFFRACTION3A
4X-RAY DIFFRACTION4A
5X-RAY DIFFRACTION5A
6X-RAY DIFFRACTION6B
7X-RAY DIFFRACTION7B
8X-RAY DIFFRACTION8B
9X-RAY DIFFRACTION9B
10X-RAY DIFFRACTION10B
11X-RAY DIFFRACTION11B
12X-RAY DIFFRACTION12B

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