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- PDB-8clz: Crystal structure of Rhizobium etli constitutive L-asparaginase R... -

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Basic information

Entry
Database: PDB / ID: 8clz
TitleCrystal structure of Rhizobium etli constitutive L-asparaginase ReAIV (monoclinic form R4mC-2)
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: 1.501 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
DepositionFeb 17, 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 1.3Nov 6, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
BBB: Putative L-asparaginase II protein
AAA: Putative L-asparaginase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5419
Polymers72,2332
Non-polymers3087
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-150 kcal/mol
Surface area23170 Å2
Unit cell
Length a, b, c (Å)96.245, 85.298, 82.946
Angle α, β, γ (deg.)90.000, 109.178, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-676-

HOH

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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 / Plasmid: pEt-151D-topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 Gold / References: UniProt: Q2KB35
#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.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium formate, 20 % (w/v) PEG 3350, and 0.2% lauryldimethylamine oxide (LDAO)

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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: 0.977 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2021
RadiationMonochromator: 0.977 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.5→78.34 Å / Num. obs: 100056 / % possible obs: 99.1 % / Redundancy: 2.99 % / Biso Wilson estimate: 26.72 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.107 / Net I/σ(I): 6.6
Reflection shellResolution: 1.5→1.59 Å / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 16066 / CC1/2: 0.517 / Rrim(I) all: 1.044

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.501→78.34 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.365 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3024 1000 1 %
Rwork0.2533 99046 -
all0.254 --
obs-100046 99.172 %
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: 22.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.903 Å20 Å2-0.16 Å2
2--1.462 Å20 Å2
3----1.815 Å2
Refinement stepCycle: LAST / Resolution: 1.501→78.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 7 376 5313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135049
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154784
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.6356834
X-RAY DIFFRACTIONr_angle_other_deg1.3191.57211001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.88520.65246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75415811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg141542
X-RAY DIFFRACTIONr_chiral_restr0.070.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021154
X-RAY DIFFRACTIONr_nbd_refined0.1950.21056
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24491
X-RAY DIFFRACTIONr_nbtor_refined0.1530.22417
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2313
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.120.23
X-RAY DIFFRACTIONr_metal_ion_refined0.210.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.214
X-RAY DIFFRACTIONr_nbd_other0.1810.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.215
X-RAY DIFFRACTIONr_mcbond_it1.462.2832681
X-RAY DIFFRACTIONr_mcbond_other1.4522.2822680
X-RAY DIFFRACTIONr_mcangle_it2.1393.4233352
X-RAY DIFFRACTIONr_mcangle_other2.1423.4243353
X-RAY DIFFRACTIONr_scbond_it1.8212.4812368
X-RAY DIFFRACTIONr_scbond_other1.8212.4812368
X-RAY DIFFRACTIONr_scangle_it2.6983.653477
X-RAY DIFFRACTIONr_scangle_other2.6973.6513478
X-RAY DIFFRACTIONr_lrange_it3.91328.0455629
X-RAY DIFFRACTIONr_lrange_other3.81327.8795580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.501-1.540.469720.4227211X-RAY DIFFRACTION98.2198
1.54-1.5820.443730.4117149X-RAY DIFFRACTION99.7652
1.582-1.6280.407700.3956985X-RAY DIFFRACTION99.7032
1.628-1.6780.352670.3746665X-RAY DIFFRACTION98.7242
1.678-1.7330.456670.3496568X-RAY DIFFRACTION99.8345
1.733-1.7940.39640.3256357X-RAY DIFFRACTION99.705
1.794-1.8620.343610.3086088X-RAY DIFFRACTION99.8052
1.862-1.9380.368600.2885912X-RAY DIFFRACTION99.7161
1.938-2.0240.286570.2755639X-RAY DIFFRACTION99.563
2.024-2.1220.317550.265409X-RAY DIFFRACTION99.4902
2.122-2.2370.313510.265121X-RAY DIFFRACTION99.0046
2.237-2.3730.282490.2424797X-RAY DIFFRACTION98.2762
2.373-2.5360.294460.2464568X-RAY DIFFRACTION99.4397
2.536-2.7390.329420.2464228X-RAY DIFFRACTION99.4179
2.739-3.0010.274400.2383919X-RAY DIFFRACTION99.2231
3.001-3.3540.299360.2343524X-RAY DIFFRACTION98.834
3.354-3.8720.283310.2123107X-RAY DIFFRACTION98.1852
3.872-4.7390.235260.1942594X-RAY DIFFRACTION97.037
4.739-6.690.228210.1982055X-RAY DIFFRACTION98.6692
6.69-78.340.258120.1941150X-RAY DIFFRACTION96.7527

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