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

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Basic information

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


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
ASPARTIC ACID / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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: Atomic model / Author supporting evidence ...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_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / struct_conf / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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_struct_special_symmetry.auth_seq_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5204
Polymers69,2542
Non-polymers2662
Water6,503361
1
A: L-asparaginase 2
B: L-asparaginase 2
hetero molecules

A: L-asparaginase 2
B: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0398
Polymers138,5074
Non-polymers5324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area17180 Å2
ΔGint-46 kcal/mol
Surface area39700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.384, 133.553, 63.914
Angle α, β, γ (deg.)90.000, 110.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-680-

HOH

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Components

#1: Protein L-asparaginase 2 / Asparaginase


Mass: 34626.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ansB, NCTC9075_01362 / Production host: unidentified (others) / References: UniProt: A0A377K0N3, asparaginase
#2: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: (Hampton Research) PEG-ion I 30 - 0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350

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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: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 31, 2018
RadiationMonochromator: Double Crystal Monochromator - Water-cooled Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.89→44.601 Å / Num. obs: 84730 / % possible obs: 89.8 % / Redundancy: 2.791 % / Biso Wilson estimate: 38.136 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.043 / Χ2: 1.166 / Net I/σ(I): 18.09 / Num. measured all: 236478
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
1.89-22.2340.4491.88213801525795720.8490.5762.7
2-2.142.8380.2663.763607114263127090.9450.32689.1
2.14-2.312.90.1616.483691613339127290.9830.19795.4
2.31-2.532.740.1049.723242712268118350.990.12996.5
2.53-2.832.9980.05916.583225711092107600.9960.07297
2.83-3.262.8320.03526.3926838982894760.9980.04496.4
3.26-3.992.8150.02240.422552829380120.9990.02896.6
3.99-5.622.9240.01951.8318061637061760.9990.02397
5.62-44.6012.8820.01556.959976360934610.9990.01895.9

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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: 2.1→32.024 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2771 2882 4.39 %
Rwork0.2221 62833 -
obs0.2245 65715 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.18 Å2 / Biso mean: 39.4952 Å2 / Biso min: 17.78 Å2
Refinement stepCycle: final / Resolution: 2.1→32.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 18 361 5241
Biso mean--35.44 37.97 -
Num. residues----652
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.13440.33151330.2961285791
2.1344-2.17120.3931320.3055293895
2.1712-2.21070.40921330.3158293895
2.2107-2.25320.36591370.3312301397
2.2532-2.29920.41591320.3139291696
2.2992-2.34920.32051380.2874304797
2.3492-2.40380.35241370.2956299897
2.4038-2.46390.37121390.2833299996
2.4639-2.53050.31881350.2582300398
2.5305-2.60490.32761410.261304397
2.6049-2.68890.22721390.2579301197
2.6889-2.7850.33851390.2638299397
2.785-2.89640.35891390.2704301297
2.8964-3.02820.34031390.2668301297
3.0282-3.18770.32161390.2545302096
3.1877-3.38720.34741410.2342295196
3.3872-3.64840.2241360.2169302897
3.6484-4.01490.23461400.1881301697
4.0149-4.59440.22961370.1576298697
4.5944-5.78290.17561410.1639304797
5.7829-32.020.18911350.1386300596

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