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- PDB-7os3: Crystal structure of Rhizobium etli inducible L-asparaginase ReAV... -

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Basic information

Entry
Database: PDB / ID: 7os3
TitleCrystal structure of Rhizobium etli inducible L-asparaginase ReAV solved by S-SAD (orthorhombic form START)
ComponentsL-asparaginase II protein
KeywordsHYDROLASE / L-asparaginase / amidohydrolase / Rhizobium etli / S-SAD
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 / SAD / Resolution: 2.177 Å
AuthorsGilski, M. / Loch, J.I. / Imiolczyk, B. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/37/B/NZ1/03250 Poland
Citation
Journal: Nat Commun / Year: 2021
Title: Crystal structures of the elusive Rhizobium etli L-asparaginase reveal a peculiar active site.
Authors: Loch, J.I. / Imiolczyk, B. / Sliwiak, J. / Wantuch, A. / Bejger, M. / Gilski, M. / Jaskolski, M.
#1: Journal: Acta Biochim Pol / Year: 2001
Title: Sequence analysis of enzymes with asparaginase activity
Authors: Borek, D. / Jaskolski, M.
History
DepositionJun 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,3116
Polymers79,1102
Non-polymers2024
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-109 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.150, 91.050, 105.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein L-asparaginase II protein


Mass: 39554.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Class 3 (R. etli) type L-asparaginase
Source: (gene. exp.) Rhizobium etli (strain CFN 42 / ATCC 51251) (bacteria)
Strain: CFN 42 / ATCC 51251 / Gene: ansA, RHE_PE00350 / Plasmid: pET151D-TOPO / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Magic / References: UniProt: Q2K0Z2
#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.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 0.2 M Li2SO4, 0.01% (w/v) heptane-1,2,3-triol, 0.1 M Tris pH 8.0

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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: 2.0664 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0664 Å / Relative weight: 1
ReflectionResolution: 2.177→69.024 Å / Num. obs: 75182 / % possible obs: 98.3 % / Redundancy: 17.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.74
Reflection shellResolution: 2.18→2.23 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 4503 / CC1/2: 0.85 / % possible all: 79.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.177→69.024 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.244 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.189
Details: Hydrogens were added at their riding positions. Bijvoet pairs were merged for refinement.
RfactorNum. reflection% reflection
Rfree0.2238 1000 2.52 %
Rwork0.1677 38687 -
all0.169 --
obs-39687 98.611 %
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: 34.053 Å2
Baniso -1Baniso -2Baniso -3
1--3.307 Å2-0 Å2-0 Å2
2---2.432 Å20 Å2
3---5.738 Å2
Refinement stepCycle: LAST / Resolution: 2.177→69.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5321 0 4 314 5639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135412
X-RAY DIFFRACTIONr_bond_other_d00.0175123
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.6377315
X-RAY DIFFRACTIONr_angle_other_deg1.3181.58211766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0045715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58620.212283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66115877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.471554
X-RAY DIFFRACTIONr_chiral_restr0.0520.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026247
X-RAY DIFFRACTIONr_gen_planes_other00.021237
X-RAY DIFFRACTIONr_nbd_refined0.2120.21231
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.25013
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22685
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2312
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.210
X-RAY DIFFRACTIONr_nbd_other0.2020.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2460.214
X-RAY DIFFRACTIONr_mcbond_it2.7162.8962869
X-RAY DIFFRACTIONr_mcbond_other2.7122.8952867
X-RAY DIFFRACTIONr_mcangle_it3.8284.3373581
X-RAY DIFFRACTIONr_mcangle_other3.8254.3373581
X-RAY DIFFRACTIONr_scbond_it4.273.3562543
X-RAY DIFFRACTIONr_scbond_other4.2693.3562544
X-RAY DIFFRACTIONr_scangle_it6.3044.8463734
X-RAY DIFFRACTIONr_scangle_other6.3044.8473735
X-RAY DIFFRACTIONr_lrange_it8.39136.1976097
X-RAY DIFFRACTIONr_lrange_other8.34435.9756045
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.177-2.2340.336600.28923530.2929360.7380.76682.18670.261
2.234-2.2950.346720.24527750.24728490.7830.84299.92980.222
2.295-2.3620.204700.20727160.20727910.8730.88499.82090.187
2.362-2.4340.266670.19826010.226880.8730.9199.2560.173
2.434-2.5140.264670.18825640.1926320.8810.91699.9620.168
2.514-2.6020.271640.17724830.17925470.9020.9271000.157
2.602-2.70.209620.16123920.16324540.9290.9431000.142
2.7-2.810.221590.16223090.16323690.9310.94999.95780.144
2.81-2.9350.221570.15222030.15422600.940.9571000.137
2.935-3.0780.231550.16521260.16721810.930.9461000.148
3.078-3.2440.245530.16320300.16520830.9280.9511000.153
3.244-3.440.2490.15319020.15519560.9510.96399.74440.147
3.44-3.6770.156470.14318170.14418640.9680.9691000.141
3.677-3.9710.203440.13516940.13717380.9580.9731000.138
3.971-4.3480.214400.13815650.13916050.9590.9731000.146
4.348-4.8590.22370.14314230.14514620.9620.9799.86320.162
4.859-5.6060.188330.17212620.17212950.980.9651000.186
5.606-6.8550.217270.19110790.19211060.9410.961000.208
6.855-9.6470.219230.1558680.1578910.9510.9731000.181
9.647-69.0240.254140.2045250.2055390.9490.9621000.245
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1875-0.19780.01020.5437-0.0150.08480.0347-0.0172-0.0191-0.025-0.03260.0163-0.0064-0.0231-0.00220.0550.01720.00020.0654-0.00160.003142.009655.090622.4594
20.1759-0.1391-0.07010.30510.02260.16380.0223-0.02750.0291-0.0411-0.0365-0.02640.03030.0430.01420.05010.01670.00880.06590.00860.011675.736638.808521.0849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA-3 - 367
2X-RAY DIFFRACTION2ALLBBB4 - 352

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