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- PDB-6uod: Asparaginase II from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 6uod
TitleAsparaginase II from Escherichia coli
ComponentsL-asparaginase 2
KeywordsHYDROLASE / asparaginase / cancer / Acute lymphoblastic leukemia
Function / homology
Function and homology information


cellular anatomical entity / asparagine metabolic process / asparaginase / asparaginase activity
Similarity search - Function
L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like ...L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile.
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsAraujo, T.S. / Almeida, M.S. / Lima, L.M.T.R.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Biophys.Chem. / Year: 2021
Title: Biophysical characterization of two commercially available preparations of the drug containing Escherichia coli L-Asparaginase 2.
Authors: de Araujo, T.S. / Scapin, S.M.N. / de Andrade, W. / Fasciotti, M. / de Magalhaes, M.T.Q. / Almeida, M.S. / Lima, L.M.T.R.
History
DepositionOct 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Oct 6, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / struct_conf / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_gene_src_gene / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_validate_torsion.auth_comp_id / _refine.B_iso_mean / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _struct_conf.end_auth_comp_id / _struct_conf.end_label_comp_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Description: Sequence discrepancy / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase 2
B: L-asparaginase 2
C: L-asparaginase 2
D: L-asparaginase 2


Theoretical massNumber of molelcules
Total (without water)138,4474
Polymers138,4474
Non-polymers00
Water8,557475
1
A: L-asparaginase 2
B: L-asparaginase 2

A: L-asparaginase 2
B: L-asparaginase 2


Theoretical massNumber of molelcules
Total (without water)138,4474
Polymers138,4474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14320 Å2
ΔGint-55 kcal/mol
Surface area40070 Å2
MethodPISA
2
C: L-asparaginase 2

C: L-asparaginase 2

D: L-asparaginase 2

D: L-asparaginase 2


Theoretical massNumber of molelcules
Total (without water)138,4474
Polymers138,4474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_565-x,y+1,-z1
Buried area14500 Å2
ΔGint-54 kcal/mol
Surface area40730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.215, 60.084, 142.786
Angle α, β, γ (deg.)90.000, 117.990, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-asparaginase 2


Mass: 34611.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ansB, NCTC10418_01397 / Production host: unidentified (others) / References: UniProt: A0A376KNM9, asparaginase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.2 M Magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3,350, L-Aspartic 1 mM

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen gas / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4588 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 30, 2018
RadiationMonochromator: Double Crystal Monochromator - Water-cooled Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4588 Å / Relative weight: 1
ReflectionResolution: 2.31→47.108 Å / Num. obs: 87788 / % possible obs: 90 % / Redundancy: 1.695 % / Biso Wilson estimate: 41.218 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.047 / Χ2: 1.101 / Net I/σ(I): 13.85 / Num. measured all: 148792
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.31-2.451.4740.1423.531772215713120270.9670.19376.5
2.45-2.621.6720.1075.152386514803142750.9780.14696.4
2.62-2.831.7510.0847.332296513760131160.9870.11495.3
2.83-3.11.6880.0610.631974412715116960.9940.08292
3.1-3.471.7970.03816.581945011470108210.9970.05294.3
3.47-41.7120.03221.73142621013583330.9970.04482.2
4-4.891.7130.02227.8913406856978270.9980.03191.3
4.89-6.881.8090.02128.8311451664363290.9980.02995.3
6.88-47.1081.7620.01735.065927373933640.9990.02390

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSVERSION Jan 26, 2018 BUILT=20180808data reduction
XDSVERSION Jan 26, 2018 BUILT=20180808data scaling
MrBUMP00.9.00phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ihd

1ihd


Resolution: 2.4→38.578 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 3005 3.71 %
Rwork0.1984 77957 -
obs0.2004 80962 92.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.01 Å2 / Biso mean: 36.9742 Å2 / Biso min: 16.96 Å2
Refinement stepCycle: final / Resolution: 2.4→38.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9284 0 0 475 9759
Biso mean---35.57 -
Num. residues----1240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.43930.32581140.2542350289
2.4393-2.48140.34151630.2503389195
2.4814-2.52650.32791530.2481384097
2.5265-2.57510.31431380.2337389797
2.5751-2.62770.32331450.2394390196
2.6277-2.68480.28411530.2316377896
2.6848-2.74720.3541330.2345384695
2.7472-2.81590.33931660.246381995
2.8159-2.8920.20791310.2317372394
2.892-2.97710.29181510.2345373392
2.9771-3.07310.32351310.2334358791
3.0731-3.18290.29631630.2275383695
3.1829-3.31030.28131260.2134380495
3.3103-3.46090.28551630.2201375894
3.4609-3.64320.2361250.2207344687
3.6432-3.87120.2631250.2178314978
3.8712-4.16980.21181340.1819348388
4.1698-4.58880.18921490.1574369791
4.5888-5.25140.20491430.1465379196
5.2514-6.61080.24261570.1593382996
6.6108-38.5780.14581420.1314364791

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