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- PDB-9qct: Crystal structure of Rhizobium etli L-asparaginase ReAV R47A mutant -

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Basic information

Entry
Database: PDB / ID: 9qct
TitleCrystal structure of Rhizobium etli L-asparaginase ReAV R47A mutant
ComponentsL-asparaginase II
KeywordsHYDROLASE / Rhizobium etli / amidohydrolases / L-asparaginases / site-directed mutagenesis
Function / homologyL-asparaginase II / L-asparaginase II / L-asparaginase II
Function and homology information
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
C: L-asparaginase II
D: L-asparaginase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,84836
Polymers157,8754
Non-polymers1,97332
Water26,7521485
1
A: L-asparaginase II
B: L-asparaginase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,91118
Polymers78,9382
Non-polymers97316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-82 kcal/mol
Surface area25790 Å2
2
C: L-asparaginase II
D: L-asparaginase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,93718
Polymers78,9382
Non-polymers1,00016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-65 kcal/mol
Surface area25610 Å2
Unit cell
Length a, b, c (Å)78.059, 91.550, 114.462
Angle α, β, γ (deg.)90.000, 96.900, 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

#1: Protein
L-asparaginase II


Mass: 39468.754 Da / Num. of mol.: 4 / Mutation: R47A
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
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 1485 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 22% PEG 4000, 0.2 M MgCl2, 0.1 M Bicine pH 9.0, 1% v/v isopropanol

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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: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.75→71.29 Å / Num. obs: 160568 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 18.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.135 / Net I/σ(I): 8.38
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 25814 / CC1/2: 0.57 / Rrim(I) all: 1.057

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→50.6 Å / SU ML: 0.2189 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2109 1001 0.62 %
Rwork0.1709 159484 -
obs0.1712 160485 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.08 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10316 0 113 1485 11914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011910864
X-RAY DIFFRACTIONf_angle_d1.10614688
X-RAY DIFFRACTIONf_chiral_restr0.06931632
X-RAY DIFFRACTIONf_plane_restr0.01071953
X-RAY DIFFRACTIONf_dihedral_angle_d13.31054060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.840.30841420.275122568X-RAY DIFFRACTION98.99
1.84-1.960.28861430.229622792X-RAY DIFFRACTION99.88
1.96-2.110.23181420.189922747X-RAY DIFFRACTION99.8
2.11-2.320.23581430.1722810X-RAY DIFFRACTION99.81
2.32-2.660.21641430.163722783X-RAY DIFFRACTION99.68
2.66-3.350.21641430.163222858X-RAY DIFFRACTION99.69
3.35-50.60.16031450.143422926X-RAY DIFFRACTION98.92
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)
10.9543257956351.94031351509-0.1988177404645.10424355857-0.8688662788851.22741767846-0.04697464805040.105615090748-0.0351070353178-0.05105766918680.06887681052550.141408392986-0.03296775487090.0231076810428-0.0278086776540.09393857057690.00745239335694-0.006637113423090.132480471534-0.004178436725740.10741392539-9.0603728902846.8597957083-7.89283197865
20.9628780556530.160330333321-0.3214729702541.08895163166-0.4578802436641.933549779050.0236981832208-0.04936151054250.03251992801230.0894938220837-0.005638246661390.0506040546674-0.0273430651228-0.0518620061562-0.0222963057070.133455443192-0.0166210177777-0.009484929383930.114997357297-0.001957085659920.153231950995-4.2788004317666.049094558714.9402699134
32.43465925033-0.6871604709530.1474284523121.405577313650.1226001153691.35671833961-0.01271356133860.0554248156474-0.0241149942993-0.0119266327340.0113501628338-0.118584197398-0.04124126279870.1689323527680.006406672855830.123326490701-0.03621406837250.01374374035520.1117982354770.002917667793830.1679794851883.2588196024962.42350660130.361684985778
40.8006971682750.5881438886050.3216901083111.005383304010.1527022402610.42471825303-0.007549667325910.0257258826948-0.1296198607890.04057026978070.0201211118772-0.1259206854480.05717693176380.0292369302915-0.001538661361110.1128133677360.01476739075640.007170126760640.119990338504-0.00945073407550.175744699082-2.1099930042143.7606011832.86251952228
57.673254465117.457565066041.230293550277.516120889361.39899236221.02911396325-0.1655983547090.194828980790.150241333149-0.1699832004330.1273004250920.0586461898045-0.0332356553018-0.02315430060750.03173930729690.1107900773730.010560077144-0.01692701276430.1415555812180.01557060990720.165094462728-25.316091583251.7175060273-6.79771829724
60.4285902095030.418931474692-0.5222745157961.10526703478-0.7844716162470.749578227778-0.0460142354110.0775304258772-0.030970730659-0.02259193049190.04743995666990.1004507227950.0578809519992-0.130551296668-0.01441872851390.130123797517-0.0429799964801-0.01090979356220.185340906012-0.0333184231090.169887370344-40.139868070331.61318097690.810802335337
72.576731299530.6119706783660.209365038992.845392317160.3771854021821.771214959980.031208995999-0.04468113099760.0522855912710.168164251044-0.0133411049228-0.16594054055-0.05637996307570.115444906157-0.03007605230080.139108406497-0.02550386751560.004400670227870.1352950802550.005189040519980.10010694383-33.746400774730.865695649419.3082872915
81.43869355636-1.032422427790.5829488503191.6057922183-1.072522278661.47943988213-0.01237522055740.0941483101799-0.0200643922534-0.176601054296-0.0185770247456-0.00172903110260.229118131762-0.1261258797630.03882968551640.158504524284-0.07202587928750.001839951770450.162813250436-0.03288536573350.14545242093-37.853875778827.7793691123-0.921261953731
91.981299803040.6020282933780.271358924793.350449918220.09864440492311.25163028658-0.04318416744020.0765535265881-0.06278982138420.05423261579610.01410608693040.2820660628680.0383175906314-0.3883545868790.06505284446010.109051409481-0.01968567852120.02584435028950.2330576958320.001288600049990.176513732621-46.326671413839.8193824337.6571656065
104.445327261350.5324551897870.717278869362.197329737260.2600970388171.46180512982-0.06120852184330.1497463103240.0434312943994-0.07015779603570.07920648482040.0545654702401-0.0353593593615-0.14779400658-0.01201315346260.101446614396-0.001026474439630.00924342624280.1556244406860.02578392635280.109014185365-38.726038530346.5232754724-3.32417275274
112.368945835891.543687553171.244708496681.940198779261.447753282621.89973019206-0.0157070636427-0.1167670256180.0511961042149-0.02696001615860.03966969888350.100704656416-0.0724432870672-0.0649616235533-0.01783445336520.1636120268150.0291882505434-0.02160335261540.1188058645670.03296229524970.219964697643-32.977033265658.12390942851.02639507114
122.96411508442-2.39258151875-0.6840934633254.047291554520.8508812686661.05745220603-0.0701121090185-0.102606839144-0.1239091054230.09884650817010.02761413624470.0863380055744-0.0067644986161-0.01176703138610.04223613437430.116695220184-0.0133397728269-0.002921764143760.1286332335320.006156869492640.1017316514162.2559047759544.328371153864.5272247944
132.28231883393-0.69943877325-0.7767863300631.195628576270.6210056207141.519968211110.01989895268270.103143594309-0.0165861390242-0.0375439152573-0.06061456380020.0490208823099-0.00116768590639-0.07038549837610.04655382639720.1423713853370.00501774548022-0.009775203508690.1002289019180.005247662318360.113366249838-4.813917350763.076894106440.2323587434
143.57293157357-1.86125525182-1.5839131345.330734361761.988575827743.403688444370.1772351904220.261722652556-0.266025669034-0.283755394852-0.153644127612-0.1894499003350.04421207101190.227278124067-0.01764907220850.1637958001160.0211092505374-0.02590122563460.198072408202-0.007340601199910.1396757211683.3314284468659.134918809936.9036119643
150.5966161347340.0243065814254-0.1776235010791.19472701411-0.06378939294060.781230329453-0.00965771812234-0.00196561434880.02789867901610.007310526837520.008030126176950.0527634366298-0.0205000219434-0.02937038997180.0008316929470060.1410441278430.01685065642932.02079854324E-50.139556473240.003821626061340.158769402906-7.7334264622160.212521534152.850859233
162.54147504368-0.877048708599-0.5714820382421.48326773060.3057800039660.851981965877-0.05731762163650.0600152012376-0.1068897620440.02727872261860.02078647143630.1469824507610.064899906115-0.03614223892920.04919055195870.11783093216-0.005429601525470.0007679144728890.1020408890550.01424835886490.142954870184-3.8104361781639.68007639156.6147264854
174.27581214935-5.653813156391.906877904947.54450907343-2.493758961980.8585688629-0.124292227994-0.108522008205-0.02088505887390.2115787266420.1529170917650.149459874642-0.0743150893180.0288518523324-0.0324212141810.153912597876-0.005285463760890.001057330573210.187270662712-0.006863432865480.18080806243918.626216714149.204998932163.3830621698
180.58257909411-1.0629258901-1.137603280542.40229613351.908645164192.62264422555-0.0186317453513-0.02681848547050.01459539809230.01562775344320.0346886579136-0.06253853764040.01750495978070.133057661165-0.02710146847980.1268539860890.00601898769102-0.006536751793080.1795708340.03309020669880.14782669804332.924888599628.395478944355.8807140045
192.377919408120.0906900378658-0.07328582428121.79990892929-0.1811071427831.81409400444-0.01406349053760.1024442975230.186842192363-0.153863810446-0.05229507038750.151122118534-0.163536508783-0.1222924942640.04364416502370.181991529360.0370897188288-0.006062427592830.1395977204760.01817624615560.12211834399726.108286181732.072801089135.4091520311
200.5620331995680.154204247589-0.1488423389641.143339576530.2317605216440.979691130918-0.0128887307567-0.04194698530190.0123888172242-0.02705501933330.0149689981241-0.1174450083290.03371531625840.0930844927496-5.86245630638E-50.1196637204490.0202874533303-0.001852314693630.1620291279980.01780110972890.15470924271733.312704472327.580092160551.3982880595
215.61943181729-0.7994173711430.7516029214821.790010107150.07163710576611.32990917189-0.0125448196834-0.166350405714-0.06192305465420.05512103451330.050562764926-0.206836777483-0.06751633246960.145347071982-0.03585672340550.109117728945-0.004348585097320.006439176623240.148059228212-0.0137472140550.14608728443731.786125348243.48244626359.9001879877
223.33218824962-2.330837019651.923133111422.41104726322-1.259695890082.283910677680.0158719434140.1567776240750.254910622501-0.00221423110531-0.00335896278014-0.234749067386-0.03844214483140.0457522239591-0.002069343097330.166813248306-0.0359681493311-0.002585503261710.119847342273-0.01059600081490.20613623062426.013819507155.459022462855.4025189752
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 46 )AA4 - 461 - 43
22chain 'A' and (resid 47 through 175 )AA47 - 17544 - 172
33chain 'A' and (resid 176 through 237 )AA176 - 237173 - 234
44chain 'A' and (resid 238 through 352 )AA238 - 352235 - 349
55chain 'B' and (resid 4 through 28 )BH4 - 281 - 25
66chain 'B' and (resid 29 through 70 )BH29 - 7026 - 67
77chain 'B' and (resid 71 through 161 )BH71 - 16168 - 158
88chain 'B' and (resid 162 through 216 )BH162 - 216159 - 213
99chain 'B' and (resid 217 through 265 )BH217 - 265214 - 262
1010chain 'B' and (resid 266 through 313 )BH266 - 313263 - 310
1111chain 'B' and (resid 314 through 352 )BH314 - 352311 - 349
1212chain 'C' and (resid 4 through 46 )CR4 - 461 - 43
1313chain 'C' and (resid 47 through 114 )CR47 - 11444 - 111
1414chain 'C' and (resid 115 through 149 )CR115 - 149112 - 146
1515chain 'C' and (resid 150 through 265 )CR150 - 265147 - 262
1616chain 'C' and (resid 266 through 352 )CR266 - 352263 - 349
1717chain 'D' and (resid 4 through 28 )DZ4 - 281 - 25
1818chain 'D' and (resid 29 through 70 )DZ29 - 7026 - 67
1919chain 'D' and (resid 71 through 135 )DZ71 - 13568 - 132
2020chain 'D' and (resid 136 through 265 )DZ136 - 265133 - 262
2121chain 'D' and (resid 266 through 314 )DZ266 - 314263 - 311
2222chain 'D' and (resid 315 through 352 )DZ315 - 352312 - 349

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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