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- PDB-6vin: Crystallographic structure of the circularly permuted human Taspa... -

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Basic information

Entry
Database: PDB / ID: 6vin
TitleCrystallographic structure of the circularly permuted human Taspase1 protein
ComponentsThreonine aspartase 1
KeywordsHYDROLASE / Taspase1 / enzyme / asparaginase / X-ray structure.
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 / cytosol / cytoplasm
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: 3.04 Å
AuthorsMartin-Garcia, J.M. / Fromme, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)NX118-107-160-007 United States
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
DepositionJan 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 1.2Aug 18, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 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
B: Threonine aspartase 1


Theoretical massNumber of molelcules
Total (without water)82,4792
Polymers82,4792
Non-polymers00
Water00
1
A: Threonine aspartase 1
B: Threonine aspartase 1

A: Threonine aspartase 1
B: Threonine aspartase 1

A: Threonine aspartase 1
B: Threonine aspartase 1


Theoretical massNumber of molelcules
Total (without water)247,4386
Polymers247,4386
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20880 Å2
ΔGint-82 kcal/mol
Surface area86260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.000, 196.000, 196.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Threonine aspartase 1 / Taspase-1


Mass: 41239.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TASP1, C20orf13 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9H6P5, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases

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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: 4.3 Å3/Da / Density % sol: 70 %
Description: Cuboids of size range between 200 and 500 microns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M sodium citrate pH 4.0, 1.0 M ammonium sulfate, 10% 2-methyl-2,4-pentanediol (MPD), and 0.4 M NaCl
PH range: 4.0-4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.04→49.05 Å / Num. obs: 15315 / % possible obs: 93.9 % / Redundancy: 19.6 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.2
Reflection shellResolution: 3.04→3.11 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 15315

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UGK

6ugk


Resolution: 3.04→49.05 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.74
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3074 1568 10.2 %RANDOM
Rwork0.2366 ---
obs0.2435 13749 54.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 462.8 Å2 / Biso mean: 152.987 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 3.04→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5349 0 0 0 5349
Num. residues----728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135447
X-RAY DIFFRACTIONr_bond_other_d0.0360.0175096
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.6327348
X-RAY DIFFRACTIONr_angle_other_deg2.4691.57411826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3925723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31522.08250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.09715880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5221534
X-RAY DIFFRACTIONr_chiral_restr0.0660.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026205
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021101
LS refinement shellResolution: 3.04→3.116 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.36 15 -
Rwork0.313 110 -
obs--6.02 %

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