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- PDB-9qcw: Crystal structure of Rhizobium etli L-asparaginase ReAV K51A mutant -

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Basic information

Entry
Database: PDB / ID: 9qcw
TitleCrystal structure of Rhizobium etli L-asparaginase ReAV K51A mutant
ComponentsL-asparaginase II
KeywordsHYDROLASE / Rhizobium etli / amidohydrolases / L-asparaginases / site-directed mutagenesis
Function / homologyL-asparaginase II / L-asparaginase II / DI(HYDROXYETHYL)ETHER / L-asparaginase II
Function and homology information
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPokrywka, K. / Grzechowiak, M. / Loch, J.I. / Ruszkowski, M. / Gilski, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/37/B/NZ1/03250 Poland
Citation
Journal: Biomolecules / Year: 2025
Title: Probing the Active Site of Class 3 L-Asparaginase by Mutagenesis: Mutations of the Ser-Lys Tandems of ReAV.
Authors: Pokrywka, K. / Grzechowiak, M. / Sliwiak, J. / Worsztynowicz, P. / Loch, J.I. / Ruszkowski, M. / Gilski, M. / Jaskolski, M.
#1: Journal: IUCrJ / Year: 2021
Title: Structural and biophysical aspects of l-asparaginases: a growing family with amazing diversity.
Authors: Loch, J.I. / Jaskolski, M.
#2: Journal: Nat. Comm. / 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.
#3: Journal: Acta Cryst. D / 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.
#4: Journal: Front. Chem. / Year: 2024
Title: Probing the active site of Class 3 L-asparaginase by mutagenesis. I. Tinkering with the zinc coordination site of ReAV.
Authors: Pokrywka, K. / Grzechowiak, M. / Sliwiak, J. / Worsztynowicz, P. / Loch, J.I. / Ruszkowski, M. / Gilski, M. / Jaskolski, M.
History
DepositionMar 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 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.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,68226
Polymers79,0442
Non-polymers1,63824
Water8,395466
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-75 kcal/mol
Surface area25790 Å2
Unit cell
Length a, b, c (Å)78.003, 91.271, 106.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-asparaginase II


Mass: 39521.793 Da / Num. of mol.: 2 / Mutation: K51A, H238Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Gene: ansA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RFN5

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Non-polymers , 6 types, 490 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4000, 0.2 M Li2SO4, 0.1 M Tris pH 8.5

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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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→91.27 Å / Num. obs: 55856 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Rrim(I) all: 0.155 / Net I/σ(I): 10.75
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.046 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 8876 / CC1/2: 0.819 / Rrim(I) all: 1.132

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→69.2 Å / SU ML: 0.2388 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3061
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2283 999 1.79 %
Rwork0.1811 54777 -
obs0.1819 55776 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.54 Å2
Refinement stepCycle: LAST / Resolution: 1.95→69.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 97 466 5867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01095563
X-RAY DIFFRACTIONf_angle_d1.14617502
X-RAY DIFFRACTIONf_chiral_restr0.0766829
X-RAY DIFFRACTIONf_plane_restr0.0113994
X-RAY DIFFRACTIONf_dihedral_angle_d13.14042062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.050.35271400.27587690X-RAY DIFFRACTION99
2.05-2.180.28991410.23237725X-RAY DIFFRACTION99.43
2.18-2.350.27481400.20867747X-RAY DIFFRACTION99.67
2.35-2.580.24011430.19367787X-RAY DIFFRACTION99.62
2.58-2.960.21321420.17977813X-RAY DIFFRACTION99.81
2.96-3.730.22961440.16327882X-RAY DIFFRACTION99.79
3.73-69.20.18211490.15328133X-RAY DIFFRACTION99.42
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)
15.700116614846.907495132462.412677863538.586913870092.604366277072.16705471659-0.2493116709910.2175331867960.121166802459-0.4233314864380.1467508533550.269488857451-0.144314771425-0.04411988025210.07345264464020.1523197814060.0187880322010.007713343303280.17306923152-0.01869411079180.25523148976514.21959273377.0925522458519.5641366776
21.240004518240.655861718222-0.4688902143842.37910685738-1.465148914671.246380011840.04577363100550.00371617916212-0.1683787288560.0550495307343-0.03566481043330.3235295512580.0361082986171-0.219219269202-0.02314192884250.195324920709-0.04865449106130.01732682222740.219187750522-0.1007801205990.311482326552-1.11138862669-13.167958653127.1421634475
32.553541402171.673091635591.906128678383.558937104811.896140131141.701321537390.0749044362449-0.18076617239-0.1344346678370.351310840961-0.0419460637198-0.2438607482340.061955776874-0.024748409977-0.02351975524930.317334263545-0.07955452160650.08233244661980.262069871048-0.0004366867258290.2745216754215.50646455046-14.327253518145.8676621701
41.57161196536-0.3748991229370.2912610016451.24373535958-0.7426545369041.18036630832-0.01232460846740.060816780775-0.127213295929-0.048005197853-0.1095438969350.1431325191080.332151475207-0.2296985151790.1132995710720.227876013141-0.1010611449840.02222365251230.248919079215-0.06131841212350.2720077848880.824050089838-16.927100417325.6255544822
50.8730129107231.101848081370.2250215337693.46125626329-1.074619309280.985046996074-0.07935708800960.0625286765824-0.1085950257640.1801977443790.005701935677260.3868793451870.0162185019183-0.4798879023650.05438695217510.20423491075-0.05080319582180.1009564105980.362661345276-0.1067312406590.390743047832-7.01649841679-5.1295056966734.5496293943
62.12867937690.5912333612910.279502827181.227036982980.2106916773511.194939779330.0272391198403-0.04222950934140.2547183771460.0117092527088-0.06263795770740.245007578448-0.0546909791768-0.2136704085640.04603267894050.1609405575210.007616986666860.01807011278090.212026104896-0.03216023375250.3207988175672.936168651736.697405476425.3950816252
72.453731888090.857126466209-0.3417094261613.25333148289-0.204159316721.44682079141-0.1145360640620.173909526102-0.127735893993-0.407033306051-0.0140557145375-0.07771905431150.02879844321390.04669407488060.1174306601890.1590700666260.0214427139842-0.00978885227990.1533684925280.005994756486040.1771292437129.77340068880.42317307540316.7457297596
81.587480159530.528071657301-0.2708394356591.82635807514-0.2785538383041.67364356190.11578042236-0.2136741551830.0384467127720.323252400363-0.1264645399240.1255847186620.0113887510344-0.0811462528714-0.005446033988170.219726351792-0.05252200768020.008706239597730.168680837518-0.02161876770860.22862314181334.882364927520.771227218341.6723173014
91.197361995120.4095979408730.1766840377851.595927506810.298960386160.915627672327-0.004983851647620.00873174616033-0.1268796267230.06420747883420.0111506107243-0.2946064404180.05617858391030.1415736861190.003919147673120.144533529266-0.01059580868637.53531568024E-50.1505408827020.01188868938750.23942797436440.63354674729.1553155065328.2346691381
100.0456651615772-0.0486136783778-0.2794969896181.28440854688-1.146855259313.17468141439-0.04274088093-0.232264256834-0.5998426842520.0969032227953-0.192831307106-0.5278010333770.0951086235660.2225182646050.2381231243480.2354838524280.008070921485370.0250848901670.1819732416740.03206172936390.38545254897532.5736755972-10.739455288733.7961508701
113.544647505411.99889219419-2.725546050314.18982445771-4.420175378285.45233700659-0.07466768242930.5820992751670.0407992998951-0.350488727230.0707817281670.360366333230.13878524443-0.2511527655930.05790091295140.333492084602-0.0269465235317-0.04402672273950.287767880445-0.07482456411610.39886098948231.6149888284-3.3761014505210.6337437596
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 27 )AA3 - 271 - 25
22chain 'A' and (resid 28 through 70 )AA28 - 7026 - 68
33chain 'A' and (resid 71 through 161 )AA71 - 16169 - 159
44chain 'A' and (resid 162 through 216 )AA162 - 216160 - 214
55chain 'A' and (resid 217 through 265 )AA217 - 265215 - 263
66chain 'A' and (resid 266 through 352 )AA266 - 352264 - 350
77chain 'B' and (resid -3 through 46 )BL-3 - 461 - 50
88chain 'B' and (resid 47 through 175 )BL47 - 17551 - 179
99chain 'B' and (resid 176 through 314 )BL176 - 314180 - 318
1010chain 'B' and (resid 315 through 341 )BL315 - 341319 - 345
1111chain 'B' and (resid 342 through 367 )BL342 - 367346 - 366

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