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- PDB-4osx: STRUCTURE of UNCLEAVED GLYCINE-BOUND HUMAN L-ASPARAGINASE PROTEIN -

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Basic information

Entry
Database: PDB / ID: 4osx
TitleSTRUCTURE of UNCLEAVED GLYCINE-BOUND HUMAN L-ASPARAGINASE PROTEIN
ComponentsIsoaspartyl peptidase/L-asparaginase
KeywordsHYDROLASE / NTN ENZYME
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: Chem.Biol. / Year: 2013
Title: Free Glycine Accelerates the Autoproteolytic Activation of Human Asparaginase.
Authors: Su, Y. / Karamitros, C.S. / Nomme, J. / Mcsorley, T. / Konrad, M. / Lavie, A.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionMar 5, 2014ID: 4HLO
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

Downloads & links

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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)64,8879
Polymers64,4652
Non-polymers4217
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-20 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.940, 59.940, 301.100
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: 32232.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALP, ASRGL1, 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.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 293 K / pH: 7
Details: 2.2 M SODIUM MALONATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
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
111.000H, 1.000K, L10.5
11-1.000H-1.000K, 1.000K, -L20.5
ReflectionResolution: 1.95→51.91 Å / Num. obs: 43500 / % possible obs: 94.7 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2 Å / % possible all: 90

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GDT

4gdt
PDB Unreleased entry


Resolution: 1.95→29.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.502 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2248 5.2 %RANDOM
Rwork0.167 ---
obs0.169 41251 98 %-
all-41251 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.24 Å20 Å20 Å2
2---4.24 Å20 Å2
3---8.49 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 27 176 4565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224488
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9666071
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.435610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96225.06166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0515757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4981520
X-RAY DIFFRACTIONr_chiral_restr0.0920.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213340
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5331.52981
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94424740
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46431507
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1714.51324
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 194 -
Rwork0.228 2727 -
obs--88.19 %

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