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- PDB-9thy: ReAIV structure containing an acrylamide adduct at Cys183 and an ... -

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Basic information

Entry
Database: PDB / ID: 9thy
TitleReAIV structure containing an acrylamide adduct at Cys183 and an orthoborate ester at Ser47
ComponentsL-asparaginase II protein
KeywordsHYDROLASE / L-asparaginase / acrylamide / zinc metalloenzyme / adduct / microcalorimetry / ITC
Function / homologyL-asparaginase II / L-asparaginase II / metal ion binding / PROPIONAMIDE / L-asparaginase II protein
Function and homology information
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSliwiak, J. / Grzechowiak, M. / Worsztynowicz, P. / Pokrywka, K. / Ruszkowski, M. / Gilski, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/37/B/NZ1/03250. Poland
CitationJournal: Amino Acids / Year: 2026
Title: Efficient acrylamide adduct formation suggests dual applications of ReAIV L-asparaginase.
Authors: Sliwiak, J. / Grzechowiak, M. / Worsztynowicz, P. / Pokrywka, K. / Ruszkowski, M. / Gilski, M. / Jaskolski, M.
History
DepositionDec 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,37325
Polymers72,3222
Non-polymers1,05023
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-205 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.415, 80.453, 142.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-asparaginase II protein


Mass: 36161.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Gene: RHE_CH01144 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2KB35

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Non-polymers , 6 types, 772 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ROP / PROPIONAMIDE


Mass: 73.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H7NO / Source: (gene. exp.) Rhizobium etli (bacteria) / Gene: RHE_CH01144 / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM bicine buffer, 200 mM MgCl 2 , 25% PEG 8000, 0.5% DDM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.39→46.48 Å / Num. obs: 105422 / % possible obs: 95 % / Redundancy: 11.4 % / CC1/2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 1.39→1.51 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5272 / CC1/2: 0.509

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Processing

Software
NameVersionClassification
PHENIX1.21.2-5419refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→34.07 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 1114 1.06 %
Rwork0.137 --
obs0.137 105412 74.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→34.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 46 749 5815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055396
X-RAY DIFFRACTIONf_angle_d0.7927338
X-RAY DIFFRACTIONf_dihedral_angle_d14.8951987
X-RAY DIFFRACTIONf_chiral_restr0.078814
X-RAY DIFFRACTIONf_plane_restr0.007983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.460.4556130.23441282X-RAY DIFFRACTION7
1.46-1.540.2416700.20436438X-RAY DIFFRACTION37
1.54-1.630.24331280.179212086X-RAY DIFFRACTION70
1.63-1.760.22081520.158514674X-RAY DIFFRACTION85
1.76-1.940.18341820.144416990X-RAY DIFFRACTION98
1.94-2.220.17891870.124817390X-RAY DIFFRACTION100
2.22-2.790.16341890.139217480X-RAY DIFFRACTION100
2.79-34.070.18221930.129517958X-RAY DIFFRACTION100

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