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- PDB-9bad: Crystal structure of Bacillus subtilis 168 L-asparaginase II with... -

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Basic information

Entry
Database: PDB / ID: 9bad
TitleCrystal structure of Bacillus subtilis 168 L-asparaginase II with antileukemic activity
ComponentsL-asparaginase 2
KeywordsANTITUMOR PROTEIN / Enzyme / Leukemia / Recombinant
Function / homology
Function and homology information


L-asparagine catabolic process / asparaginase / asparaginase activity / periplasmic space
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 speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGomes, J.G.S. / Rocha, B.A.M. / Brandao, L.C. / Furtado, G.P. / Pontes, L.Q. / Lourenzoni, M.R.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)313837/2020-1 Brazil
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural and biochemical characterization of a thermostable Bacillus subtilis L-asparaginase with antiproliferative effects on hematological cancer cell lines.
Authors: Brandao, L.C. / da Silva Gomes, J.G. / Pinheiro, D.P. / Caetano, L.F. / Bezerra, M.R.L. / Pontes, L.Q. / Pinheiro, M.P. / de Aquino, A.V.F.G. / Silva, J.M.F. / Souza, P.F.N. / Furtado, C.L.M. ...Authors: Brandao, L.C. / da Silva Gomes, J.G. / Pinheiro, D.P. / Caetano, L.F. / Bezerra, M.R.L. / Pontes, L.Q. / Pinheiro, M.P. / de Aquino, A.V.F.G. / Silva, J.M.F. / Souza, P.F.N. / Furtado, C.L.M. / Pessoa, C.D.O. / Lourenzoni, M.R. / da Rocha, B.A.M. / Furtado, G.P.
History
DepositionApr 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,0017
Polymers159,8634
Non-polymers1383
Water20,2491124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint-45 kcal/mol
Surface area40250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.234, 104.486, 123.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-asparaginase 2 / L-ASNase 2 / L-asparagine amidohydrolase 2


Mass: 39965.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Bacillus Genetic Stock Center
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: ansZ, yccC, BSU02690 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: O34482, asparaginase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.06 Å3/Da / Density % sol: 40.17 % / Description: Cubic to rectangular crystals
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 400 25 %, HEPES 0.1 M, NaCl 0.1 M

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen jet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.3→48.135 Å / Num. obs: 321574 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.99 / Net I/av σ(I): 11.3 / Net I/σ(I): 1.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 31082 / CC1/2: 0.54 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDS1.08data reduction
pointless1.12.12data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→48.13 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.618 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16433 16178 5 %RANDOM
Rwork0.13552 ---
obs0.13695 305395 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.358 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å20 Å2
2---0.45 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.3→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9427 0 8 1124 10559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0129724
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169386
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.6513230
X-RAY DIFFRACTIONr_angle_other_deg0.5891.57421663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29651296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.308536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.803101674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.21594
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022018
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_it4.9021.5515139
X-RAY DIFFRACTIONr_mcbond_other4.9021.5515139
X-RAY DIFFRACTIONr_mcangle_it6.9332.7896450
X-RAY DIFFRACTIONr_mcangle_other6.9322.7896451
X-RAY DIFFRACTIONr_scbond_it7.6051.874585
X-RAY DIFFRACTIONr_scbond_other7.6031.874585
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.7973.2926781
X-RAY DIFFRACTIONr_long_range_B_refined14.59316.710818
X-RAY DIFFRACTIONr_long_range_B_other13.40915.8710545
X-RAY DIFFRACTIONr_rigid_bond_restr4.06319110
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 1203 -
Rwork0.253 22394 -
obs--99.99 %

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