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- PDB-8osw: Crystal structure of Rhizobium etli L-asparaginase ReAIV (R4mC-1) -

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Basic information

Entry
Database: PDB / ID: 8osw
TitleCrystal structure of Rhizobium etli L-asparaginase ReAIV (R4mC-1)
ComponentsPutative L-asparaginase II protein
KeywordsHYDROLASE / amidohydrolase / zinc binding protein / structural homology / enzymatic mechanism / enzyme kinetics / occluded water molecules
Function / homologyL-asparaginase II / L-asparaginase II / metal ion binding / L-asparaginase II protein
Function and homology information
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLoch, J.I. / Worsztynowicz, P. / Sliwiak, J. / Imiolczyk, B. / Grzechowiak, M. / Gilski, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/37/B/NZ1/03250 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Rhizobium etli has two L-asparaginases with low sequence identity but similar structure and catalytic center.
Authors: Loch, J.I. / Worsztynowicz, P. / Sliwiak, J. / Grzechowiak, M. / Imiolczyk, B. / Pokrywka, K. / Chwastyk, M. / Gilski, M. / Jaskolski, M.
History
DepositionApr 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Structure summary / Category: audit_author / chem_comp_atom / chem_comp_bond / Item: _audit_author.name
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,5058
Polymers72,2332
Non-polymers2736
Water15,691871
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-136 kcal/mol
Surface area24100 Å2
Unit cell
Length a, b, c (Å)95.762, 85.889, 82.723
Angle α, β, γ (deg.)90.000, 108.720, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Putative L-asparaginase II protein


Mass: 36116.391 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
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M MgCl2, 17.5% PEG 8000, 0.3% DDM, 100 mM Asp

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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: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.3→78.35 Å / Num. obs: 150517 / % possible obs: 96.6 % / Redundancy: 6.27 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.086 / Net I/σ(I): 14.2
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 4.51 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 19954 / CC1/2: 0.791 / Rrim(I) all: 0.655 / % possible all: 79.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→46.2 Å / SU ML: 0.1294 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1629 1001 0.67 %
Rwork0.1335 149502 -
obs0.1337 150503 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.37 Å2
Refinement stepCycle: LAST / Resolution: 1.3→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5021 0 6 871 5898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01155596
X-RAY DIFFRACTIONf_angle_d1.2527634
X-RAY DIFFRACTIONf_chiral_restr0.1031845
X-RAY DIFFRACTIONf_plane_restr0.01141028
X-RAY DIFFRACTIONf_dihedral_angle_d10.0232839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.370.28111130.240716919X-RAY DIFFRACTION76.72
1.37-1.450.18341470.139422036X-RAY DIFFRACTION100
1.45-1.570.17491480.115422022X-RAY DIFFRACTION100
1.57-1.720.16161470.121322021X-RAY DIFFRACTION100
1.72-1.970.16021480.12222079X-RAY DIFFRACTION99.98
1.97-2.480.15511480.135222132X-RAY DIFFRACTION99.97
2.48-46.20.1541500.13322293X-RAY DIFFRACTION99.91

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