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- PDB-2a8m: Crystal Structure of Human Taspase1 (T234S mutant) -

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Basic information

Entry
Database: PDB / ID: 2a8m
TitleCrystal Structure of Human Taspase1 (T234S mutant)
ComponentsThreonine aspartase 1
KeywordsHYDROLASE / Taspase / MLL / Leukemia / Asparaginase
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 / SAD / Resolution: 2.6 Å
AuthorsKhan, J.A. / Dunn, B.M. / Tong, L.
CitationJournal: Structure / Year: 2005
Title: Crystal Structure of Human Taspase1, a Crucial Protease Regulating the Function of MLL.
Authors: Khan, J.A. / Dunn, B.M. / Tong, L.
History
DepositionJul 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0704
Polymers88,9992
Non-polymers712
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-40 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.441, 89.371, 104.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Threonine aspartase 1 / Taspase 1


Mass: 44499.441 Da / Num. of mol.: 2 / Mutation: T234S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf13 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H6P5, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 1.8 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 294 K / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9798
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2005 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 16867 / % possible obs: 93.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.0097
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.96 / % possible all: 73.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBTHEN SOLVE/RESOLVEphasing
CNS1.1refinement
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.59 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 245503.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1596 10 %RANDOM
Rwork0.207 ---
obs0.207 15899 88.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0479 Å2 / ksol: 0.349278 e/Å3
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1--15.07 Å20 Å20 Å2
2--23.12 Å20 Å2
3----8.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4512 0 2 109 4623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.375 125 11 %
Rwork0.259 1008 -
obs--63.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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