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- PDB-8rud: Crystal structure of Rhizobium etli L-asparaginase ReAV K138A mutant -

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Basic information

Entry
Database: PDB / ID: 8rud
TitleCrystal structure of Rhizobium etli L-asparaginase ReAV K138A mutant
ComponentsL-asparaginase II protein
KeywordsHYDROLASE / Rhizobium etli / amidohydrolases / l-asparaginases / zinc-binding proteins / site-directed mutagenesis
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: 2.1 Å
AuthorsPokrywka, K. / Grzechowiak, M. / Sliwiak, J. / Worsztynowicz, P. / 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: 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.
#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 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.
#3: Journal: 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
DepositionJan 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase II protein
B: L-asparaginase II protein
C: L-asparaginase II protein
D: L-asparaginase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,66830
Polymers157,9874
Non-polymers1,68126
Water13,007722
1
A: L-asparaginase II protein
B: L-asparaginase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,77214
Polymers78,9942
Non-polymers77812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-9 kcal/mol
Surface area25410 Å2
MethodPISA
2
C: L-asparaginase II protein
D: L-asparaginase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,89616
Polymers78,9942
Non-polymers90314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-2 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.066, 91.386, 114.547
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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L-asparaginase II protein


Mass: 39496.770 Da / Num. of mol.: 4 / Mutation: K138A
Source method: isolated from a genetically manipulated source
Details: point mutation K138A / Source: (gene. exp.) Rhizobium etli (bacteria) / Gene: ansA, RHE_PE00350 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2K0Z2

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Non-polymers , 5 types, 748 molecules

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


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 22% PEG 3350, 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: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→113.73 Å / Num. obs: 91345 / % possible obs: 97.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 23.13 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.168 / Net I/σ(I): 7.72
Reflection shellResolution: 2.1→2.23 Å / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 14875 / CC1/2: 0.571 / Rrim(I) all: 1.046

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→56.86 Å / SU ML: 0.3468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Hydrogen atoms were added at riding position.
RfactorNum. reflection% reflection
Rfree0.2618 999 1.1 %
Rwork0.2059 90120 -
obs0.2066 91119 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→56.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10330 0 106 722 11158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009610812
X-RAY DIFFRACTIONf_angle_d1.072114609
X-RAY DIFFRACTIONf_chiral_restr0.05881620
X-RAY DIFFRACTIONf_plane_restr0.011942
X-RAY DIFFRACTIONf_dihedral_angle_d14.8674017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.33451430.296612946X-RAY DIFFRACTION98.93
2.21-2.350.40681350.311212103X-RAY DIFFRACTION92.3
2.35-2.530.3041430.249412895X-RAY DIFFRACTION98.35
2.53-2.790.26951440.228313056X-RAY DIFFRACTION99.39
2.79-3.190.29491460.196213121X-RAY DIFFRACTION99.66
3.19-4.020.2241420.174212838X-RAY DIFFRACTION97.42
4.02-56.860.19561460.154913161X-RAY DIFFRACTION98.38
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)
16.469538109444.949733686260.7773234447174.18830510740.6030973082840.735762750468-0.4327366652540.176634637561-0.252124912179-0.3664830886540.266644659821-0.176277536743-0.0724279952592-0.05992991143870.1739691601410.1494196819180.00659787575184-0.001620847880.1753275188190.01199764818270.222611074513-25.503326222351.4125475153-7.04566758082
21.4362696851.2160987587-1.400134954042.5159812768-2.061322135242.39766842097-0.04611192855270.0738596220485-0.000189674353834-0.06158553390570.03122817323870.07252248585330.148181552578-0.132594385297-0.004005202432580.16591065309-0.02498973695510.006536510759450.151335019838-0.03997308349170.190797746108-39.611630759831.67726709490.712487550095
33.675079668420.186238068050.1209389763172.22524145969-0.3399789140841.77994352063-0.0318920253015-0.05901374268870.2748674731120.0819102497894-0.0453636437425-0.118747060784-0.1764028063510.1163236419580.08346023913560.234822606652-0.04260877601110.03746596987850.196766558895-0.02753663433320.205153331913-33.086258534935.073799639221.576960758
42.510547812492.033145358341.172510816794.596787031060.8945851686453.516168813310.1136345558170.0242114634662-0.5284213911720.105029022038-0.0353389024995-0.8589136391060.332315228693-0.015815774529-0.05591784652190.195190067110.0132763506546-0.0008536737630850.1718735186350.008174684577910.244400258188-35.37284263219.351501668514.0475207699
52.00656997144-0.6415404067350.351621506281.7739994363-1.311893524791.83517405414-0.03926959312540.03335215097140.0384216521796-0.2257675149250.0140557168873-0.108355570330.294038818331-0.2044121667870.05702498185330.208512572685-0.09034013259740.02252933881930.227199528005-0.04568860127280.257282378032-38.266702822928.0607928839-0.870186936966
62.089337838931.922055549361.93527303758.389711159131.001299327623.17222411217-0.02183624837120.281176443454-0.3071020865070.0148860584099-0.2262442285440.395875719840.0955229802352-1.059739190020.1649530800020.179816122859-0.06273085749090.06874573917790.440163791511-0.02907926296420.443881006083-52.139621489132.72059044674.96810684782
71.13895466460.525478251387-0.1494062929391.209695558570.1482270655020.982653572047-0.004396230555250.02366486330470.1450875318950.0323636614351-0.001858800208050.19749124604-0.0382732943102-0.133814439810.01753790448040.1835568995610.01888559172530.009258760941230.1938029500410.009570163275790.274550954582-37.420143548650.11393211811.43982962143
85.865624400716.55748594164-2.059726312397.80919050298-2.857758130361.35926641307-0.1660786842090.215106514812-0.148075271384-0.4767716137640.1939302855930.02949015782420.10319968518-0.0735349563311-0.05538417006860.2067374153210.02164921829090.02923262053830.191663140675-0.04435713368760.232965096804-13.432517848641.1160058606-6.11831135207
91.387809378170.9392812915711.878753491776.234229098140.2220294682312.74103829051-0.1822795548110.28270363669-0.0302532408517-0.4974704204980.0876534638590.140365235512-0.09990344833520.2630942589120.09335582063440.207265566034-0.0007164248828510.01392654519740.1609954509220.02792810086040.164700111505-2.9593205459553.9850834154-10.6202112076
101.213190825150.885818100974-0.4584955772610.8169820068850.01495057095511.471336705450.0433195036442-0.08693136604080.08430098638150.0603212300427-0.0636116278252-0.0130360468377-0.03956414446650.03917737413210.01530200753460.209909160497-0.0155783618354-0.00106716239390.1619494735360.007323919337490.244664385981-1.7179419292664.561695294116.4284235115
115.696328398534.81678408854-2.794403811827.03872768721-3.727086135914.382562522430.115202418699-0.06610227078470.05404505568340.001110867579040.1035582158990.3640034955830.166898933763-0.1930598593-0.2339679708040.2017880755660.00562994708987-0.002303457625810.1915517542820.00116310065480.217625700769-9.7474883372961.052338733220.1710171991
120.6096769324350.05767057630270.1049852982551.09124904470.3700847516960.807616996810.00914546021614-0.000600104281936-0.00293332742355-0.03163634276770.0227736167975-0.1122341269090.02042629951790.079433574963-0.02857675128980.157619262217-0.01273133797160.03250009397850.1667645614350.00644747174860.2543757636150.63486878770257.62853886472.07647744507
131.740077058231.77410727024-1.017332856152.01866191605-0.9807447514511.894691584830.114873633983-0.126069913697-0.119854305454-0.0124986372535-0.0585855338504-0.1861642331220.0473209394608-0.0192307734942-0.06015843768160.1980751879630.01958672395850.05678028410.165884202606-0.009537305201020.336817947269-6.7431641335535.55056609482.867949903
146.88345219379-6.497776012312.057421123496.85460413993-2.467186759721.16805760219-0.442124864695-0.363100758683-0.01453936903650.4769353193910.429668631182-0.146306907952-0.243930782205-0.0528830504612-0.01260742220910.2457991955710.006581260193340.04388375300230.220978130474-0.02828674574150.3227556109318.848303276148.821662282863.8964102121
152.113200673440.200746201109-1.51760901977.653512154690.3595689464961.6411105131-0.0900019556572-0.3740499867980.1519883306470.4316290566710.04628134148810.2635243634860.03790242851460.3083758295220.06010414032380.207964846352-6.12822008604E-50.004376681342580.2579550566440.02076658644010.15812612490428.622572005635.228082475867.4183737215
161.514741988410.2817310660770.867356205830.867520367256-0.5737100205052.303687537340.004235463145580.07159325808620.0319640803721-0.122201334374-0.0130605239378-0.182090842064-0.00902024029160.114272138190.01225509464440.2378143359160.0232119799390.04755497120560.19829442682-0.001389888883520.28787851796831.458077292227.126977002740.0231599369
174.27639451891-3.675708003332.233505958948.49763410389-3.933455486624.28459326560.3176473699590.01456299853890.29258715983-0.446679402582-0.2149338145470.1456665861060.0402334725706-0.24914369463-0.08614064125010.2349808927690.01415248081370.1145570391750.242690042108-0.001087125732680.33563614753923.607129979331.084761575736.2378226337
180.7356122621250.30607226842-0.01742242022681.772099305620.1178883422180.5273243420260.00693313375279-0.05355802204940.0156448737421-0.01353223603810.0104547887978-0.1390387281250.02183115494710.143283676843-0.01149044922970.1836783931690.01238743354390.03198658589630.2289258290130.01206959413790.26615884183733.135232805133.058434178754.6717201106
194.15789671269-3.125834649592.827298241852.52744404379-1.713564806672.86981699622-0.002344781570750.2141469912770.0107425481574-0.09801876070820.00298507415877-0.02275386879710.05157774676190.09207607142270.003201729758030.266241374963-0.03609883864510.07369118100570.191701938297-0.01399025015540.33967466301626.111231980455.407293714955.5373588328
204.36164105031-5.46743636861-2.713547502526.878438333593.261340170272.39984270369-0.330853125998-0.528327443038-0.1065747245660.2352199914070.357787540607-0.08142942570720.03495650226020.375337863453-0.06802689204270.1928583784190.002603608557770.04586291668210.2019824751610.01403941646530.3158071082516.5286392919138.664594786862.8519686761
212.16173376961-0.6539703151690.5708457427671.27754256073-1.194595100091.12255500780.00863486051124-0.399053937426-0.008023496568320.20248813795-0.06661574412950.186419899253-0.131342617924-0.1057032469910.03735800833270.2493896204850.008169810418180.08583051943510.233389888711-0.07431218590260.257414443586-3.4678967791352.217571824767.2741483128
221.405317161670.783196401291-0.8062494570270.477079678239-0.1784087478442.26895009983-0.0249403803930.0686279012384-0.00674901408275-0.07336929931440.011843201190.0355160111180.0283800238846-0.01951316905760.009354936117390.2219990153840.0241298878476-0.0007316423014820.150344379275-0.009491594860340.250653957496-4.7798235774962.681516267640.573184093
234.25495547978-2.24230313868-1.488748673463.745372354291.516162217853.577441180380.04352327907880.306640548847-0.3833598792950.04791863096480.0339653945820.007923314945910.09939918821240.227934429727-0.06168058528210.2194681416860.0261546382540.0104952491040.266916190383-0.01768967893110.2462407440393.1796192903159.123060635136.6951504866
240.9982782457160.03921055086840.01238505380592.08815784237-0.3192493414641.385300450110.01227764666760.05329881951610.1314408235840.0418821115184-0.03198412056940.1919090743290.02058551199820.04029571784240.01287160502040.1819951770230.01315998475360.04179790637810.186222033129-0.006445096018770.264989657714-7.430021545164.111730635255.1168067481
250.888689209023-0.518518236548-0.1487131870290.987440486259-0.1298710325110.600578635838-0.006664038438560.0951970087654-0.0896855425186-0.0337087329317-0.02412005220020.1685180377360.0243370957746-0.07808667956610.03070887055640.227648799901-0.004017028196640.0265234149090.186423422216-0.00199466854930.334086946955-4.7111568111941.474122223653.9205802925
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 28 )AA4 - 281 - 25
22chain 'A' and (resid 29 through 70 )AA29 - 7026 - 67
33chain 'A' and (resid 71 through 135 )AA71 - 13568 - 132
44chain 'A' and (resid 136 through 161 )AA136 - 161133 - 158
55chain 'A' and (resid 162 through 217 )AA162 - 217159 - 214
66chain 'A' and (resid 218 through 237 )AA218 - 237215 - 234
77chain 'A' and (resid 238 through 353 )AA238 - 353235 - 350
88chain 'B' and (resid 4 through 28 )BF4 - 281 - 25
99chain 'B' and (resid 29 through 46 )BF29 - 4626 - 43
1010chain 'B' and (resid 47 through 114 )BF47 - 11444 - 111
1111chain 'B' and (resid 115 through 149 )BF115 - 149112 - 146
1212chain 'B' and (resid 150 through 314 )BF150 - 314147 - 311
1313chain 'B' and (resid 315 through 352 )BF315 - 352312 - 349
1414chain 'C' and (resid 4 through 28 )CQ4 - 281 - 25
1515chain 'C' and (resid 29 through 46 )CQ29 - 4626 - 43
1616chain 'C' and (resid 47 through 114 )CQ47 - 11444 - 111
1717chain 'C' and (resid 115 through 149 )CQ115 - 149112 - 146
1818chain 'C' and (resid 150 through 314 )CQ150 - 314147 - 311
1919chain 'C' and (resid 315 through 352 )CQ315 - 352312 - 349
2020chain 'D' and (resid 4 through 28 )DZ4 - 281 - 25
2121chain 'D' and (resid 29 through 46 )DZ29 - 4626 - 43
2222chain 'D' and (resid 47 through 114 )DZ47 - 11444 - 111
2323chain 'D' and (resid 115 through 149 )DZ115 - 149112 - 146
2424chain 'D' and (resid 150 through 237 )DZ150 - 237147 - 234
2525chain 'D' and (resid 238 through 352 )DZ238 - 352235 - 349

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