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

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Basic information

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


cellular anatomical structure / asparagine metabolic process / asparaginase / 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
FORMIC ACID / L-asparaginase / asparaginase
Similarity search - Component
Biological speciesBacillus paralicheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.978 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 15, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,25815
Polymers82,8112
Non-polymers44613
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-84 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.940, 91.940, 231.516
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-599-

HOH

21A-707-

HOH

31B-746-

HOH

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Components

#1: Protein L-asparaginase


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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.95 Å3/Da / Density % sol: 58.36 %
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→49.029 Å / Num. obs: 93591 / % possible obs: 98.9 % / Redundancy: 23.6 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 20.5
Reflection shellResolution: 1.8→2.02 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3638 / CC1/2: 0.826 / Rpim(I) all: 0.235 / % possible all: 82.6

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Processing

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

7c91


Resolution: 1.978→49.029 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.165 / Average fsc free: 0.946 / Average fsc work: 0.9519 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1874 3438 4.955 %
Rwork0.1673 65950 -
all0.168 --
obs-69388 98.819 %
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: 32.464 Å2
Baniso -1Baniso -2Baniso -3
1-0.281 Å2-0 Å2-0 Å2
2--0.281 Å2-0 Å2
3----0.563 Å2
Refinement stepCycle: LAST / Resolution: 1.978→49.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 25 459 5404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135022
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174698
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.6456794
X-RAY DIFFRACTIONr_angle_other_deg2.31.5810876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91522.713247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32715843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.721528
X-RAY DIFFRACTIONr_chiral_restr0.0920.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025676
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021028
X-RAY DIFFRACTIONr_nbd_refined0.2030.21044
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.24649
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22567
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2402
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.150.225
X-RAY DIFFRACTIONr_nbd_other0.1550.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.224
X-RAY DIFFRACTIONr_mcbond_it2.9093.4112566
X-RAY DIFFRACTIONr_mcbond_other2.9093.4112567
X-RAY DIFFRACTIONr_mcangle_it3.65.0883204
X-RAY DIFFRACTIONr_mcangle_other3.65.093205
X-RAY DIFFRACTIONr_scbond_it3.7523.6442456
X-RAY DIFFRACTIONr_scbond_other3.7323.6442445
X-RAY DIFFRACTIONr_scangle_it5.0775.3263590
X-RAY DIFFRACTIONr_scangle_other5.0825.3263591
X-RAY DIFFRACTIONr_lrange_it5.84141.0625799
X-RAY DIFFRACTIONr_lrange_other5.84241.0435796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.978-2.030.282150.2514071X-RAY DIFFRACTION84.1878
2.03-2.0850.2482420.2034747X-RAY DIFFRACTION99.98
2.085-2.1460.2072320.1874612X-RAY DIFFRACTION100
2.146-2.2120.2242280.1854472X-RAY DIFFRACTION100
2.212-2.2840.2112100.1764362X-RAY DIFFRACTION100
2.284-2.3640.192280.1654219X-RAY DIFFRACTION100
2.364-2.4530.2042310.1654025X-RAY DIFFRACTION100
2.453-2.5540.1871950.1683942X-RAY DIFFRACTION100
2.554-2.6670.1721880.173766X-RAY DIFFRACTION100
2.667-2.7970.2021850.1683611X-RAY DIFFRACTION100
2.797-2.9480.2031810.1743440X-RAY DIFFRACTION100
2.948-3.1270.181710.1773266X-RAY DIFFRACTION100
3.127-3.3420.1861800.1763050X-RAY DIFFRACTION100
3.342-3.610.1731600.1632879X-RAY DIFFRACTION100
3.61-3.9530.1831340.1482673X-RAY DIFFRACTION100
3.953-4.4190.1521230.132424X-RAY DIFFRACTION100
4.419-5.10.15990.1362189X-RAY DIFFRACTION100
5.1-6.2410.1871090.1791835X-RAY DIFFRACTION100
6.241-8.8020.178880.1761465X-RAY DIFFRACTION100
8.802-49.0290.225390.198902X-RAY DIFFRACTION98.9485

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