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- PDB-4o0d: Crystal structure of the human L-asparaginase protein T168S mutant -

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Basic information

Entry
Database: PDB / ID: 4o0d
TitleCrystal structure of the human L-asparaginase protein T168S mutant
ComponentsIsoaspartyl peptidase/L-asparaginase
KeywordsHYDROLASE / NTN ENZYME / HOMODIMER / asparaginase
Function / homology
Function and homology information


L-asparagine catabolic process via L-aspartate / beta-aspartyl-peptidase / Phenylalanine metabolism / asparaginase / asparaginase activity / beta-aspartyl-peptidase activity / photoreceptor inner segment / proteolysis / nucleus / cytoplasm / cytosol
Similarity search - Function
Asparaginase-like 1, metazoa / Peptidase T2, asparaginase 2 / Asparaginase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
GLYCINE / Isoaspartyl peptidase/L-asparaginase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNomme, J. / Lavie, A.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Elucidation of the Specific Function of the Conserved Threonine Triad Responsible for Human l-Asparaginase Autocleavage and Substrate Hydrolysis.
Authors: Nomme, J. / Su, Y. / Lavie, A.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoaspartyl peptidase/L-asparaginase
B: Isoaspartyl peptidase/L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7838
Polymers64,4372
Non-polymers3466
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-22 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.700, 59.700, 299.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Isoaspartyl peptidase/L-asparaginase / Asparaginase-like protein 1 / Beta-aspartyl-peptidase / Isoaspartyl dipeptidase / L-asparagine ...Asparaginase-like protein 1 / Beta-aspartyl-peptidase / Isoaspartyl dipeptidase / L-asparagine amidohydrolase / Isoaspartyl peptidase/L-asparaginase alpha chain / Isoaspartyl peptidase/L-asparaginase beta chain


Mass: 32218.615 Da / Num. of mol.: 2 / Mutation: T168S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASRGL1, ALP, CRASH / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) C41
References: UniProt: Q7L266, beta-aspartyl-peptidase, asparaginase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2-2.5 M sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2012
RadiationMonochromator: DOUBLE CRYSTAL - LIQUID NITROGEN cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.511
11K, H, -L20.489
ReflectionResolution: 1.95→30 Å / Num. all: 36456 / Num. obs: 36456 / % possible obs: 82.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.89 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.75
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.18 / % possible all: 71.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4GDV

4gdv
PDB Unreleased entry


Resolution: 1.95→29.27 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.888 / SU B: 3.595 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23401 1772 5 %RANDOM
Rwork0.17502 ---
obs0.17803 33541 80.84 %-
all-33541 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.645 Å2
Baniso -1Baniso -2Baniso -3
1--3.49 Å20 Å20 Å2
2---3.49 Å20 Å2
3---6.98 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4330 0 22 216 4568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194447
X-RAY DIFFRACTIONr_bond_other_d0.0020.024339
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9666015
X-RAY DIFFRACTIONr_angle_other_deg0.871310014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57125.061164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35415748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4991520
X-RAY DIFFRACTIONr_chiral_restr0.090.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215103
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
X-RAY DIFFRACTIONr_mcbond_it1.1061.8892408
X-RAY DIFFRACTIONr_mcbond_other1.1021.8862395
X-RAY DIFFRACTIONr_mcangle_it1.7232.8232999
X-RAY DIFFRACTIONr_mcangle_other1.7222.8222992
X-RAY DIFFRACTIONr_scbond_it1.0882.0642039
X-RAY DIFFRACTIONr_scbond_other1.0882.0642039
X-RAY DIFFRACTIONr_scangle_other1.6763.0333011
X-RAY DIFFRACTIONr_long_range_B_refined3.415.2815262
X-RAY DIFFRACTIONr_long_range_B_other3.415.2845263
LS refinement shellResolution: 1.95→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 121 -
Rwork0.22 2440 -
obs--79.14 %

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