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- PDB-9g68: Crystal structure of Rhizobium etli L-asparaginase ReAV K138A mut... -

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Basic information

Entry
Database: PDB / ID: 9g68
TitleCrystal structure of Rhizobium etli L-asparaginase ReAV K138A mutant in complex with L-Asn
ComponentsL-asparaginase II protein
KeywordsHYDROLASE / Rhizobium etli / amidohydrolases / L-asparaginases / site-directed mutagenesis
Function / homologyL-asparaginase II / L-asparaginase II / metal ion binding / ASPARAGINE / DI(HYDROXYETHYL)ETHER / L-asparaginase II protein
Function and homology information
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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: Febs J. / Year: 2025
Title: Controlling enzyme activity by mutagenesis and metal exchange to obtain crystal structures of stable substrate complexes of Class 3 l-asparaginase.
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.
#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
DepositionJul 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,54035
Polymers79,0262
Non-polymers2,51533
Water13,421745
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint58 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.142, 91.342, 106.397
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 protein


Mass: 39512.766 Da / Num. of mol.: 2 / Mutation: K138A
Source method: isolated from a genetically manipulated source
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, 778 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 20% PEG 8000, 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: 0.9196 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 1.51→69.31 Å / Num. obs: 84408 / % possible obs: 93.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 15.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.115 / Net I/σ(I): 9.6
Reflection shellResolution: 1.51→1.63 Å / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4220 / CC1/2: 0.588 / Rrim(I) all: 1.241

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→45.67 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2032 996 1.18 %
Rwork0.1713 83388 -
obs0.1716 84384 69.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.91 Å2
Refinement stepCycle: LAST / Resolution: 1.51→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5336 0 164 745 6245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00995796
X-RAY DIFFRACTIONf_angle_d1.04637829
X-RAY DIFFRACTIONf_chiral_restr0.0619871
X-RAY DIFFRACTIONf_plane_restr0.01091036
X-RAY DIFFRACTIONf_dihedral_angle_d14.6862200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.590.3018250.26972083X-RAY DIFFRACTION12.34
1.59-1.680.2515610.25095135X-RAY DIFFRACTION30.51
1.68-1.810.26441220.239610235X-RAY DIFFRACTION60.4
1.81-20.26561770.208914775X-RAY DIFFRACTION87.15
2-2.290.2162000.179216758X-RAY DIFFRACTION98.6
2.29-2.880.21852040.167117090X-RAY DIFFRACTION99.73
2.88-45.670.16632070.147417312X-RAY DIFFRACTION98.48
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)
12.494325356581.250134138610.2752779901350.964993300474-0.2367585177030.449748670443-0.09128681504980.3039538594150.00341641381262-0.1018157431970.07247467865150.101598484202-0.0164102787794-0.09390140656450.0369478528140.0523923377977-0.00638903474189-0.008460868250030.114703788068-0.03180184369310.10512368280112.9165.76118.35
20.7333137917910.376795679363-0.4539027676570.812848452035-0.2597175772590.2835173722020.04400609340090.11384407419-0.09239317947350.0333566614249-0.1381814127530.27698359580.109928808843-0.267165200412-0.03243399772820.0911899815392-0.1034493059370.04707724027350.132057194761-0.07997758501280.154455431849-0.357-13.29327.695
31.588691041820.8626482510310.804228543271.664620528960.9442648084631.061612298460.0490813060468-0.059763815134-0.09809922040810.156658064197-0.0274687219435-0.1319873798910.12269039972-0.042231676613-0.01925465183770.197075860138-0.06131659796620.05497260374770.139411429885-0.01948481284230.118403704155.721-14.40746.079
40.8162498185180.2097605857380.2948385723290.705966330685-0.3574906324690.611359525273-0.0495982763979-0.00842434956553-0.08708500585-0.00941330196885-0.06576552963010.1107261411930.310731017564-0.2623084960580.02682433808940.135621368476-0.1566468849430.01845650067840.177626430526-0.07954872117750.110560127841.261-17.16425.795
50.6463372687830.13282728976-0.2411083978720.756088054239-0.2073377455420.445784973964-0.02165644683740.0423637035479-0.09699397338050.107567222381-0.03227688551670.4019883784980.222860199256-0.65425927046-0.0680123846490.00492376416008-0.09150205815620.1381730006450.314827505438-0.1019740477770.133408139498-6.787-5.29334.766
61.257476721970.144174096785-0.2228726453321.121102676860.01471393770060.9686335015590.0524119943578-0.05611242078210.157296032406-0.000532672286014-0.09084471803770.19070790388-0.0673966049411-0.266641666538-0.0145361404730.02709582985040.003158480652990.007267828884620.136266168717-0.04877192881030.1352941470973.0655.78625.963
71.309616923940.1869242972-0.1460917899631.32604023867-0.1052833846350.861931680218-0.05984504253440.111503603713-0.0633619817109-0.2133255448410.00927657229502-0.07235262706590.04167556717060.04935807146530.03886364111860.0716729220706-0.001099507543080.007520203561470.06421804201210.0001310721060770.066833547512929.8270.47716.764
80.7430323433560.1089783112590.01353135249830.708701631546-0.06336412763820.64198339260.163648671645-0.2211006084810.07116817688010.351307427455-0.1748066662090.127586511794-0.0213481823711-0.04383614280360.01086848644660.1974713712-0.07835950682290.02217242340960.132605871734-0.01470928127210.10596841008237.4919.84543.358
91.768576804860.15967499166-0.4636364957830.475473894898-0.703163898631.077077360920.236119774989-0.253820006503-0.1712002207470.580059716571-0.2200546241650.3877437445640.122894217529-0.18747083217-0.09135361132060.306673599239-0.122404036490.09791141788810.16353161515-0.02719046357360.19152010686229.34916.02646.951
100.7284095014780.4506755680030.1000579254821.157191708350.2575157757420.6835970431430.0331745004936-0.04873036091970.0132771553880.0715415159021-0.0119631970853-0.124890575102-0.03149113368160.0866346280265-0.01412315707250.0491877811791-0.0189064742770.003021941494240.06662975161250.0007943836270030.077740087030839.69212.6728.912
111.816820622711.04432743349-1.118161352851.171800613390.4093832037432.62127161771-0.0398481132119-0.330428883592-0.6490108881730.281290085512-0.119553146224-0.5879408576870.4234044442960.4533444065160.1553344267580.181059129030.0532187270865-0.01796734645130.1569315709330.032937039560.27427540204241.373-6.90230.89
120.8071128674550.02209859289060.07517644551761.068337251110.2951219977380.8237661278020.02373406069190.0276323371192-0.0147170090854-0.0321769051448-0.048633195202-0.0403316576399-0.1460658468570.05206882896140.01928888677350.0937032073679-0.00613302991969-0.004682014148420.09260656001680.01027023481740.1324643344330.163-2.48521.919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:28 )A1 - 28
2X-RAY DIFFRACTION2( CHAIN A AND RESID 29:70 )A29 - 70
3X-RAY DIFFRACTION3( CHAIN A AND RESID 71:161 )A71 - 161
4X-RAY DIFFRACTION4( CHAIN A AND RESID 162:216 )A162 - 216
5X-RAY DIFFRACTION5( CHAIN A AND RESID 217:265 )A217 - 265
6X-RAY DIFFRACTION6( CHAIN A AND ( RESID 266:353 OR RESID 401:411 ) ) OR ( CHAIN B AND RESID 401:401 )A266 - 353
7X-RAY DIFFRACTION6( CHAIN A AND ( RESID 266:353 OR RESID 401:411 ) ) OR ( CHAIN B AND RESID 401:401 )A401 - 411
8X-RAY DIFFRACTION6( CHAIN A AND ( RESID 266:353 OR RESID 401:411 ) ) OR ( CHAIN B AND RESID 401:401 )B401
9X-RAY DIFFRACTION7( CHAIN B AND RESID -3:46 )B-3 - 46
10X-RAY DIFFRACTION8( CHAIN B AND RESID 47:114 )B47 - 114
11X-RAY DIFFRACTION9( CHAIN B AND RESID 115:149 )B115 - 149
12X-RAY DIFFRACTION10( CHAIN B AND RESID 150:313 )B150 - 313
13X-RAY DIFFRACTION11( CHAIN B AND RESID 314:329 )B314 - 329
14X-RAY DIFFRACTION12( CHAIN B AND ( RESID 330:367 OR RESID 402:419 ) )B330 - 367
15X-RAY DIFFRACTION12( CHAIN B AND ( RESID 330:367 OR RESID 402:419 ) )B402 - 419

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