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- PDB-9ufr: Crystal structure of L-asparaginase from Thermococcus Sibiricus d... -

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Basic information

Entry
Database: PDB / ID: 9ufr
TitleCrystal structure of L-asparaginase from Thermococcus Sibiricus double mutation D54G/T56Q
Componentsasparaginase
KeywordsHYDROLASE / L-asparaginase / hyperthermophilic enzyme / thermo-L-asparaginase / TsAI / point mutant / double mutation
Function / homology
Function and homology information


asparaginase / asparaginase activity / amino acid metabolic process
Similarity search - Function
Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / 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 ...Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / 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
GLYCINE / DI(HYDROXYETHYL)ETHER / asparaginase
Similarity search - Component
Biological speciesThermococcus sibiricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMatyuta, I.O. / Varfolomeeva, L.A. / Minyaev, M.E. / Dumina, M. / Zhdanov, D. / Zhgun, A. / Pokrovskaya, M. / Aleksandrova, S. / El'darov, M. / Popov, V.O. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2025
Title: Hyperthermophilic L-Asparaginase from Thermococcus sibiricus and Its Double Mutant with Increased Activity: Insights into Substrate Specificity and Structure
Authors: Dumina, M.V. / Zhdanov, D.D. / Veselovsky, A.V. / Pokrovskaya, M.V. / Aleksandrova, S.S. / Minyaev, M.E. / Varfolomeeva, L.A. / Matyuta, I.O. / Boyko, K.M. / Zhgun, A.A.
History
DepositionApr 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9294
Polymers36,6561
Non-polymers2733
Water3,963220
1
A: asparaginase
hetero molecules

A: asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8588
Polymers73,3122
Non-polymers5476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area5940 Å2
ΔGint-23 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.013, 57.447, 130.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-716-

HOH

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Components

#1: Protein asparaginase


Mass: 36655.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: G54G/T56Q / Source: (gene. exp.) Thermococcus sibiricus (archaea) / Gene: XD54_1198 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A101ELE3, asparaginase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.8 M Lithium sulfate monohydrate, 0.1 M Sodium acetate trihydrate pH 4.0 and 4% v/v Polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.9→22.7 Å / Num. obs: 27340 / % possible obs: 99.4 % / Redundancy: 12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.025 / Rrim(I) all: 0.087 / Χ2: 1.16 / Net I/σ(I): 31.5 / Num. measured all: 329002
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 96.3 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.402 / Num. measured all: 14289 / Num. unique obs: 1736 / CC1/2: 0.937 / Rpim(I) all: 0.146 / Rrim(I) all: 0.429 / Χ2: 0.85 / Net I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9UFQ

9ufq


Resolution: 1.9→22.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.482 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22525 1304 4.8 %RANDOM
Rwork0.175 ---
obs0.1774 25986 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.432 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å20 Å2
2--0.95 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.9→22.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 18 220 2749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132621
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162599
X-RAY DIFFRACTIONr_angle_refined_deg2.1461.6483551
X-RAY DIFFRACTIONr_angle_other_deg1.4581.5796010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2535340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28623.302106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36615480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6951511
X-RAY DIFFRACTIONr_chiral_restr0.1150.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022897
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02517
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_it1.3271.4711336
X-RAY DIFFRACTIONr_mcbond_other1.3271.4661334
X-RAY DIFFRACTIONr_mcangle_it2.0432.1921669
X-RAY DIFFRACTIONr_mcangle_other2.0432.1921669
X-RAY DIFFRACTIONr_scbond_it1.6971.6591284
X-RAY DIFFRACTIONr_scbond_other1.6951.6591284
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.622.3971877
X-RAY DIFFRACTIONr_long_range_B_refined4.52217.9932881
X-RAY DIFFRACTIONr_long_range_B_other4.40717.642832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 84 -
Rwork0.23 1816 -
obs--95.81 %
Refinement TLS params.Method: refined / Origin x: 12.2241 Å / Origin y: 11.4568 Å / Origin z: 9.0367 Å
111213212223313233
T0.0222 Å20.0048 Å20.0031 Å2-0.0063 Å2-0.0068 Å2--0.0218 Å2
L0.3131 °20.065 °20.2711 °2-0.2306 °20.3145 °2--0.7659 °2
S0.0119 Å °0.0092 Å °0.039 Å °0.0054 Å °-0.0124 Å °0.0092 Å °-0.0469 Å °-0.0074 Å °0.0005 Å °

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