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- PDB-8h4f: Blasnase-T13A/P55F with D-asn -

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Basic information

Entry
Database: PDB / ID: 8h4f
TitleBlasnase-T13A/P55F with D-asn
ComponentsL-asparaginase
KeywordsHYDROLASE / Mutant
Function / homology
Function and homology information


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
D-ASPARAGINE / FORMIC ACID / asparaginase
Similarity search - Component
Biological speciesBacillus paralicheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLu, F. / Wang, W. / Chi, H. / Ran, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31871742 China
CitationJournal: To Be Published
Title: Structure-based rational design of Bacillus licheniformis L-asparaginase with low/no D-asparaginase activity for a safer enzyme
Authors: Lu, F. / Wang, W. / Chi, H. / Ran, T.
History
DepositionOct 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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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)73,26415
Polymers72,5802
Non-polymers68413
Water8,125451
1
A: L-asparaginase
B: L-asparaginase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)146,52830
Polymers145,1604
Non-polymers1,36726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area22660 Å2
ΔGint-123 kcal/mol
Surface area39080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.443, 92.443, 231.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

21B-547-

HOH

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Components

#1: Protein L-asparaginase


Mass: 36290.113 Da / Num. of mol.: 2 / Mutation: T13A, P55F
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: A0A6I7U6Y2
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-DSG / D-ASPARAGINE


Type: D-peptide linking / Mass: 132.118 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H8N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: sodium formate

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.85→19.97 Å / Num. obs: 86412 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 1 / Rpim(I) all: 0.02 / Net I/σ(I): 23.6
Reflection shellResolution: 1.85→1.88 Å / Num. unique obs: 4499 / CC1/2: 0.538 / Rpim(I) all: 0.68

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C8X

7c8x


Resolution: 1.9→19.82 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2113 3880 -
Rwork0.1914 --
obs-86294 99.86 %
Displacement parametersBiso mean: 42.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 43 451 5468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01055104
X-RAY DIFFRACTIONf_angle_d1.07956897
X-RAY DIFFRACTIONf_chiral_restr0.0717770
X-RAY DIFFRACTIONf_plane_restr0.0073896
X-RAY DIFFRACTIONf_dihedral_angle_d17.60013012

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