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- PDB-9qcy: Crystal structure of Rhizobium etli L-asparaginase ReAV S80A mutant -

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Basic information

Entry
Database: PDB / ID: 9qcy
TitleCrystal structure of Rhizobium etli L-asparaginase ReAV S80A 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: 1.7 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: To Be Published
Title: Crystal structure of Rhizobium etli L-asparaginase ReAV S80A mutant
Authors: Pokrywka, K. / Grzechowiak, M. / 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

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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
C: L-asparaginase II
D: L-asparaginase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,03945
Polymers158,2834
Non-polymers2,75641
Water16,412911
1
A: L-asparaginase II
B: L-asparaginase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,56423
Polymers79,1422
Non-polymers1,42221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-90 kcal/mol
Surface area25140 Å2
MethodPISA
2
C: L-asparaginase II
D: L-asparaginase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,47522
Polymers79,1422
Non-polymers1,33320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-104 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.056, 91.482, 104.311
Angle α, β, γ (deg.)90.000, 105.610, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L-asparaginase II


Mass: 39570.867 Da / Num. of mol.: 4 / Mutation: S80A
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, 952 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 22% PEG 4000, 0.2 M Li2SO4, 0.1 M Bicine pH 9.0

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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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→75.18 Å / Num. obs: 154207 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.116 / Net I/σ(I): 7.94
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.007 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 24585 / CC1/2: 0.522 / Rrim(I) all: 1.219

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→53.66 Å / SU ML: 0.2438 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2434
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 1997 1.3 %
Rwork0.2053 152087 -
obs0.2059 154084 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→53.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10332 0 159 911 11402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110856
X-RAY DIFFRACTIONf_angle_d1.116214658
X-RAY DIFFRACTIONf_chiral_restr0.07761626
X-RAY DIFFRACTIONf_plane_restr0.01151938
X-RAY DIFFRACTIONf_dihedral_angle_d14.12054025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.32951380.327110512X-RAY DIFFRACTION96.72
1.74-1.790.38691420.307910870X-RAY DIFFRACTION99.79
1.79-1.840.3441420.285210831X-RAY DIFFRACTION99.94
1.84-1.90.28591440.259410929X-RAY DIFFRACTION99.85
1.9-1.970.28021430.234210855X-RAY DIFFRACTION99.86
1.97-2.050.27981420.215310869X-RAY DIFFRACTION99.88
2.05-2.140.25441440.207210862X-RAY DIFFRACTION99.89
2.14-2.260.23691420.196610861X-RAY DIFFRACTION99.81
2.26-2.40.25561440.18910930X-RAY DIFFRACTION99.73
2.4-2.580.21351420.199210852X-RAY DIFFRACTION99.62
2.58-2.840.30791440.202710915X-RAY DIFFRACTION99.76
2.84-3.250.22131440.202310934X-RAY DIFFRACTION99.65
3.25-4.10.22551430.176610892X-RAY DIFFRACTION99.42
4.1-53.660.20961430.189710975X-RAY DIFFRACTION98.48
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.42769586966-3.82328183841-0.215053071095.773421838530.7201684256630.183602862075-0.0540968341728-0.0687580846810.1688799966390.124428494090.0840381034503-0.3905769716850.122660405037-0.0588018318938-0.07076153670070.1137198257180.00792344930124-0.03289210892140.206578544924-0.03305753566270.31048235774913.411926187740.68148085066.05415643748
20.390127642835-0.5980853575860.5631436340821.8071072079-1.20837920061.462528598740.0131419095637-0.009460215706170.0348501732690.0299538287279-0.01645735457290.298486174278-0.115652053277-0.162565360641-0.02699366098980.1632275088420.0518264674123-0.03933775104070.239692666303-0.06620691059390.322931946894-0.56382200587961.0464810042-1.34327374883
30.970477085447-0.583982078038-0.974140668632.748914129171.01653466391.493526656180.101906375410.1165578375790.0515488286829-0.271574236112-0.0832289006085-0.157598710218-0.11796573483-0.0733764180415-0.02375905155880.2113275575840.0761975730088-0.06486730388950.243683978299-0.0172940177480.2909809587895.5640551682562.1101114769-19.684145519
41.035112791510.127075905504-0.8175663122250.963492083867-0.0664047505210.5641943317690.001020280700720.09846635740540.004639232311710.0570488414907-0.03593105997420.0854056677851-0.162532727441-0.1540455254990.02343513978410.1908705301440.0786979561074-0.04607364252540.273197172103-0.01904112183090.3448076039170.93772681075664.67791741360.677527781101
52.93929249941-1.09930680006-0.6024574159191.34736608107-0.1898944558610.5327216971360.04719713489160.06091417059810.112861998888-0.213314080673-0.2229644302140.32148514389-0.1032859441-0.4229367762450.1626189976480.1799783890350.0206931993428-0.08068313761060.364376348444-0.08089096381150.424535303356-6.6537547881853.0065406381-8.326028031
63.59693525483-0.0150704072234-0.3465011004620.363682497157-0.2590309206551.28435639596-0.0387713437371-0.0822709709082-0.209992912559-0.0574565154719-0.02491972650550.4005747107350.05294269886-0.24932872413-0.02094523979940.1138535409430.0149477348219-0.01423005854320.257526410025-0.04682725409950.4009228757380.41517749700346.03814173132.62065009116
71.26304323119-0.444184900984-0.5255252684260.07966890604210.1773681375990.8980349874080.01350357999360.168381091135-0.114988329157-0.0770424543181-0.131550414920.250932753170.0301429353264-0.276223806610.08786706013810.187533253279-0.01524914818-0.02026098025910.266593671793-0.08197094858750.5156666096336.2762709598534.5802552694-1.1622721529
85.77960350149-5.026576767042.063791027936.47962979836-1.730556855491.52828224351-0.09697417809140.2333325434870.1560890057630.166455276321-0.0788597273163-0.0108834506768-0.152108579511-0.009531072686230.1503550034790.1236877119180.00207961548481-0.008270983383360.135320128347-0.007878953302050.27034700180125.496567082751.19242187085.69281718671
93.17307420415-2.40248961833-1.081175876923.566701425521.429167877812.285355262420.000255921633922-0.4149476586140.1224278008240.179887106406-0.07340693301-0.09999467373430.1104459425470.09737690808260.03122798844040.135836238450.0106452109684-0.01908888827730.150839909610.07938830585480.26425533779135.996232820438.309575983810.4105343188
101.15098974957-0.3555760370090.9209359105191.48853523489-0.3266734201291.936204554990.0724001915240.167986863653-0.0210972165619-0.145983937559-0.0662764229399-0.0952295398890.03770117637230.0785180676916-0.0001577888071780.1466456661210.0156948506731-0.01357649386470.1894233865060.002447451578660.29435096632737.461959074327.3851581745-16.6818722686
113.87010913815-4.295562714173.390373137048.01228035457-4.575935764413.677440456060.06493750869030.02474530705690.228426500459-0.326476317512-0.06742650840270.03166267941260.0585784805536-0.0866459133948-0.01027390385390.16687258620.00397434853882-0.01957511388640.20644592440.00958769883840.27855820432929.330988175430.9855537662-19.7963754939
120.6108485009250.00537158642124-0.3910707010051.00814530020.02681352420140.856984853139-0.01866179197880.0058695250524-0.09769648934750.0009092882688810.0543221088749-0.1833102985150.04494205433790.103131885587-0.03346175440690.1509948225440.0318275028108-0.03232306642130.192411709264-0.006866314279070.37295415893440.114438398926.1740617796-1.63486744393
130.156348841526-0.4041792147970.002849704618570.8966085378980.09823014736060.456252676725-0.02815076699580.01751060080740.120603255319-0.02531034372960.0301886141937-0.181841758407-0.07043871881140.0760967831950.01565834548020.137708963319-0.0104934301348-0.02711010702610.1937365369750.01625035718610.37528169483736.983773719848.5889493507-2.82844631859
144.28676852526-5.79545508626-2.080076240267.634111685882.466354355030.999330852915-0.118293887849-0.154515351096-0.02050329185270.1687391416180.10541932737-0.02289115320470.04762022331380.117360112838-7.54277726227E-50.114168427342-0.000674716256851-0.01002532210710.185488231314-0.009257052053930.245016877957-0.55739684681939.919996293955.6752097961
150.688994908469-1.13574248651.028167678982.20420256307-2.176281939942.13086599754-0.0659295986077-0.0379198394040.06327273165210.1915672657810.1128797006030.143101448867-0.208912182467-0.131099169742-0.04575055213540.1258736191320.00719216667349-0.009068038066540.137701741329-0.02546152688290.253334878292-14.318838658260.907969167649.3345056753
162.53068458747-1.21957069091-1.152518565642.752848004780.9228965140642.341010041280.03573860090260.0815839091302-0.102673172283-0.130698119722-0.05450094275-0.0492922426602-0.01180627021690.003185249462320.01730096727730.1323555335620.0198290532876-0.02804288339150.1289034127680.008017131053540.19375937976-7.5227125590661.567596971830.1938663328
171.255438911930.0722926068357-0.3207549740971.42483962658-0.4371555004351.10591090610.007073988849270.0749216308781-0.003673781250830.0917920750112-0.006708833327550.0467429035079-0.1066136330.002744217401230.005456282698870.1289514414830.0242875389817-0.0101368849830.134710412979-0.004380870753940.245753900778-11.319905426466.789682190349.3971167673
180.796275659569-0.746999755089-0.91016041122.251622281330.4519841081982.41056981098-0.0115474740820.0533781581099-0.032496854848-0.1123009155420.0236113405970.2709899756780.0263855242691-0.254733396350.01207515826030.1268360318440.00376620905878-0.05156341084010.212917774364-0.003890449248290.313009037741-20.316920611753.506048031841.1636542904
195.645704928781.44711794043-1.706791474791.22208610991-0.7729279950133.2129151204-0.0849637913695-0.116033591688-0.3915154440260.0220213423706-0.03399743847990.2969705343870.100118600788-0.2907670877660.1279417300460.1457970496-0.00447666629515-0.009244002513620.171892514436-0.01343166896550.437268760015-20.640695144447.90108144853.4336502503
202.26343449773-0.647763548194-1.014381507031.70845701204-0.1342805704252.65572268972-0.1769218950340.176349113883-0.138193588352-0.1539002969880.03886347067350.2568130850430.239371333896-0.1108277561250.1244991362850.160600738443-0.00107427705872-3.41004599437E-50.1440377754270.01068947836220.295020153696-10.817730661741.512951449148.8916805491
213.51206263707-1.21279570357-2.530714777721.052986375411.679002008963.19439417697-0.02032165111590.108773245987-0.1414487081780.0687678710107-0.01738442876440.05052832426010.0906417034644-0.1227387891290.04636470009310.17516108780.008254545602110.005957788711470.1504822453030.005006971599580.339149675061-1.9023012886632.821763389748.3595863642
226.44293763909-7.312008476071.832056531758.62029306564-2.069233596961.31694000542-0.1586366544540.02352910741350.2585685546660.1996993367310.01596172751360.0614501760415-0.05184093870530.09088054380730.1262546443070.101970219022-0.0234501959529-0.0128752249330.1665748119490.01067879728840.24044353034511.59854984350.24103404656.9399817436
230.23783884016-0.567694647305-0.5798934102921.667251421711.153518466761.27671340797-0.00420448515065-0.0397475488563-0.01686380670860.04340587040680.0455137841019-0.2512920261620.09157768402040.228504854657-0.04492771851170.1632939233520.0544232890443-0.003959587788680.2639779877850.03310587949730.34661330423925.702184597430.135475573849.099907543
242.27076873956-1.428941347181.063093477612.94698954473-1.104509143731.947384425270.07726931533360.120774489847-0.0662702547846-0.190392928303-0.03947785717340.08877662660420.1196310831920.0276262853625-0.03706357104550.151205956410.03601689573540.01451425513060.2116641637920.001149119218670.30319494676819.495603266429.152532924130.7249832557
250.810288714747-0.0879075316386-0.302855547121.26276681081-0.001709978403491.13902007399-0.0538646114193-0.07659579451590.01229813338740.02460444608-0.00945136366227-0.213866430970.08101679318530.3201740727620.01079749720150.1321333262370.0475741451917-0.01673646524420.2979155419320.03579892312580.36939711697326.722992203136.3277103648.8249147209
262.01551089949-1.27032200970.9287735826650.78153849511-0.6210697574571.45741500657-0.005039095531570.0291128771030.1448379889020.033755140189-0.00833451475315-0.21104547199-0.01016903054380.1758169719790.01675658398610.15594973079-0.0251816812482-0.02762609183510.2256694692220.03239531376240.45684513747618.655391844856.983947839648.7207253126
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 28 )AA5 - 281 - 24
22chain 'A' and (resid 29 through 70 )AA29 - 7025 - 66
33chain 'A' and (resid 71 through 161 )AA71 - 16167 - 157
44chain 'A' and (resid 162 through 217 )AA162 - 217158 - 213
55chain 'A' and (resid 218 through 265 )AA218 - 265214 - 261
66chain 'A' and (resid 266 through 314 )AA266 - 314262 - 310
77chain 'A' and (resid 315 through 353 )AA315 - 353311 - 349
88chain 'B' and (resid 5 through 28 )BH5 - 281 - 24
99chain 'B' and (resid 29 through 46 )BH29 - 4625 - 42
1010chain 'B' and (resid 47 through 114 )BH47 - 11443 - 110
1111chain 'B' and (resid 115 through 149 )BH115 - 149111 - 145
1212chain 'B' and (resid 150 through 237 )BH150 - 237146 - 233
1313chain 'B' and (resid 238 through 352 )BH238 - 352234 - 348
1414chain 'C' and (resid 5 through 28 )CV5 - 281 - 24
1515chain 'C' and (resid 29 through 70 )CV29 - 7025 - 66
1616chain 'C' and (resid 71 through 149 )CV71 - 14967 - 145
1717chain 'C' and (resid 150 through 216 )CV150 - 216146 - 212
1818chain 'C' and (resid 217 through 265 )CV217 - 265213 - 261
1919chain 'C' and (resid 266 through 288 )CV266 - 288262 - 284
2020chain 'C' and (resid 289 through 329 )CV289 - 329285 - 325
2121chain 'C' and (resid 330 through 352 )CV330 - 352326 - 348
2222chain 'D' and (resid 4 through 28 )DD4 - 281 - 25
2323chain 'D' and (resid 29 through 70 )DD29 - 7026 - 67
2424chain 'D' and (resid 71 through 161 )DD71 - 16168 - 158
2525chain 'D' and (resid 162 through 314 )DD162 - 314159 - 311
2626chain 'D' and (resid 315 through 352 )DD315 - 352312 - 349

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