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- PDB-7cbr: Blasnase-T13A with D-asn -

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Basic information

Entry
Database: PDB / ID: 7cbr
TitleBlasnase-T13A with D-asn
ComponentsL-asparaginase
KeywordsHYDROLASE / substrate / complex / mutant
Function / homology
Function and homology information


cellular anatomical structure / asparagine metabolic process / asparaginase activity / metal ion binding
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
D-ASPARAGINE / FORMIC ACID / L-asparaginase / Asparaginase
Similarity search - Component
Biological speciesBacillus paralicheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLu, F. / Ran, T. / Jiao, L. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31871742 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Structures of l-asparaginase from Bacillus licheniformis Reveal an Essential Residue for its Substrate Stereoselectivity.
Authors: Ran, T. / Jiao, L. / Wang, W. / Chen, J. / Chi, H. / Lu, Z. / Zhang, C. / Xu, D. / Lu, F.
History
DepositionJun 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-asparaginase
B: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,43015
Polymers82,8112
Non-polymers61813
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-85 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.311, 92.311, 232.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-571-

HOH

21A-726-

HOH

31B-592-

HOH

41B-773-

HOH

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Components

#1: Protein L-asparaginase / BlAsnase


Mass: 41405.742 Da / Num. of mol.: 2 / Mutation: Y278M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus paralicheniformis (bacteria) / Gene: B4121_3474 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q8GMZ7, UniProt: A0A6I7U6Y2*PLUS
#2: Chemical ChemComp-DSG / D-ASPARAGINE


Type: D-peptide linking / Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→19.952 Å / Num. obs: 93702 / % possible obs: 99.9 % / Redundancy: 25.1 % / CC1/2: 1 / Rpim(I) all: 0.017 / Net I/σ(I): 26.9
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4554 / CC1/2: 0.84 / Rpim(I) all: 0.308

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C91

7c91


Resolution: 1.8→19.952 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1824 4589 4.903 %
Rwork0.1686 89002 -
all0.169 --
obs-93591 99.889 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.097 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0 Å2-0 Å2
2--0.66 Å2-0 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 37 505 5477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135061
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174737
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.6466847
X-RAY DIFFRACTIONr_angle_other_deg2.2861.58110975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0322.698252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67615855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2931529
X-RAY DIFFRACTIONr_chiral_restr0.0920.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025726
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021033
X-RAY DIFFRACTIONr_nbd_refined0.2070.21006
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.24582
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22556
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22476
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2391
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1890.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.221
X-RAY DIFFRACTIONr_nbd_other0.1610.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.225
X-RAY DIFFRACTIONr_mcbond_it2.6123.0982577
X-RAY DIFFRACTIONr_mcbond_other2.6113.0982578
X-RAY DIFFRACTIONr_mcangle_it3.3934.6223216
X-RAY DIFFRACTIONr_mcangle_other3.3934.6223217
X-RAY DIFFRACTIONr_scbond_it3.5073.372484
X-RAY DIFFRACTIONr_scbond_other3.5133.3722475
X-RAY DIFFRACTIONr_scangle_it4.8954.9143631
X-RAY DIFFRACTIONr_scangle_other4.8944.9143632
X-RAY DIFFRACTIONr_lrange_it5.78537.6525761
X-RAY DIFFRACTIONr_lrange_other5.71737.2115639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2913380.2786516X-RAY DIFFRACTION100
1.847-1.8970.2913080.2556313X-RAY DIFFRACTION100
1.897-1.9520.2533000.2196184X-RAY DIFFRACTION99.9846
1.952-2.0120.2182910.1955978X-RAY DIFFRACTION100
2.012-2.0780.23070.1895808X-RAY DIFFRACTION100
2.078-2.1510.1992970.1815629X-RAY DIFFRACTION100
2.151-2.2320.2032640.1775430X-RAY DIFFRACTION100
2.232-2.3230.1942970.1765210X-RAY DIFFRACTION100
2.323-2.4270.1912770.175049X-RAY DIFFRACTION99.9812
2.427-2.5450.182680.1634775X-RAY DIFFRACTION100
2.545-2.6830.1842300.1654595X-RAY DIFFRACTION100
2.683-2.8450.1792220.1674375X-RAY DIFFRACTION100
2.845-3.0410.1862130.1754103X-RAY DIFFRACTION100
3.041-3.2850.1861740.1683875X-RAY DIFFRACTION100
3.285-3.5980.1621790.1573543X-RAY DIFFRACTION100
3.598-4.0210.1541910.143228X-RAY DIFFRACTION100
4.021-4.6420.1421440.1312896X-RAY DIFFRACTION100
4.642-5.6810.1771220.1582456X-RAY DIFFRACTION100
5.681-8.0160.1861130.1841948X-RAY DIFFRACTION100
8.016-19.9520.149540.1691091X-RAY DIFFRACTION91.8941

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