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- PDB-4o0f: Crystal structure of the human L-asparaginase protein T219A mutant -

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Basic information

Entry
Database: PDB / ID: 4o0f
TitleCrystal structure of the human L-asparaginase protein T219A 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 / MOLECULAR REPLACEMENT / Resolution: 1.92 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)64,79710
Polymers64,4052
Non-polymers3928
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-29 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.471, 59.471, 299.241
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: 32202.615 Da / Num. of mol.: 2 / Mutation: T219A
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.: 4 / 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.: 155 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
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: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 6, 2012
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.512
11K, H, -L20.488
ReflectionResolution: 1.92→30 Å / Num. all: 43516 / Num. obs: 43516 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.06 / Net I/σ(I): 11.78
Reflection shellResolution: 1.92→2.04 Å / Mean I/σ(I) obs: 1.86 / Rsym value: 0.375 / % possible all: 87.6

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Processing

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

4gdv
PDB Unreleased entry


Resolution: 1.92→29.59 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.912 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21481 2214 5.1 %RANDOM
Rwork0.16461 ---
obs0.16719 40863 95.26 %-
all-40863 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.434 Å2
Baniso -1Baniso -2Baniso -3
1--3.2 Å20 Å20 Å2
2---3.2 Å20 Å2
3---6.4 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 24 155 4449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194391
X-RAY DIFFRACTIONr_bond_other_d0.0010.024287
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9685940
X-RAY DIFFRACTIONr_angle_other_deg0.94939898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8055600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01325160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31515740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0481520
X-RAY DIFFRACTIONr_chiral_restr0.0990.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02894
X-RAY DIFFRACTIONr_mcbond_it1.6952.6082379
X-RAY DIFFRACTIONr_mcbond_other1.6882.6062366
X-RAY DIFFRACTIONr_mcangle_it2.3753.9012962
X-RAY DIFFRACTIONr_mcangle_other2.3693.9012955
X-RAY DIFFRACTIONr_scbond_it1.5532.7382012
X-RAY DIFFRACTIONr_scbond_other1.5482.7382012
X-RAY DIFFRACTIONr_scangle_other2.2434.0592971
X-RAY DIFFRACTIONr_long_range_B_refined3.81521.0025119
X-RAY DIFFRACTIONr_long_range_B_other3.78620.9965102
LS refinement shellResolution: 1.92→1.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 139 -
Rwork0.194 2582 -
obs--81.54 %

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