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- PDB-9g66: Crystal structure of WT Rhizobium etli L-asparaginase ReAV in com... -

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Basic information

Entry
Database: PDB / ID: 9g66
TitleCrystal structure of WT Rhizobium etli L-asparaginase ReAV 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: 1.79 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)81,30131
Polymers79,1422
Non-polymers2,15929
Water11,440635
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint54 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.964, 91.329, 106.061
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: 39570.867 Da / Num. of mol.: 2
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 , 6 types, 664 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.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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-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: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / 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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.79→106.06 Å / Num. obs: 71415 / % possible obs: 99.5 % / Redundancy: 6 % / Biso Wilson estimate: 22.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.122 / Net I/σ(I): 10.3
Reflection shellResolution: 1.79→1.9 Å / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 2 / Num. unique obs: 11263 / CC1/2: 0.798 / Rrim(I) all: 1.037

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→45.66 Å / SU ML: 0.198 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 997 1.4 %
Rwork0.1737 70332 -
obs0.1743 71329 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.37 Å2
Refinement stepCycle: LAST / Resolution: 1.79→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5338 0 128 635 6101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01015654
X-RAY DIFFRACTIONf_angle_d1.07327615
X-RAY DIFFRACTIONf_chiral_restr0.0644845
X-RAY DIFFRACTIONf_plane_restr0.01121008
X-RAY DIFFRACTIONf_dihedral_angle_d14.50472115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.890.28091380.23939739X-RAY DIFFRACTION97.7
1.89-20.25881420.21410006X-RAY DIFFRACTION99.77
2-2.160.22811420.18999990X-RAY DIFFRACTION99.73
2.16-2.380.23761420.18379985X-RAY DIFFRACTION99.67
2.38-2.720.26561410.181610030X-RAY DIFFRACTION99.33
2.72-3.430.21681440.169810147X-RAY DIFFRACTION99.68
3.43-45.660.18061480.148910435X-RAY DIFFRACTION99.54
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)
12.40690487324-2.453617651850.4658080811463.79450647431-0.6525427042610.950530262141-0.0998334222689-0.1643458501610.0885125969180.2201960666670.0156111660974-0.1089362914760.0228452889060.112671050090.08404401356880.127086210712-0.01238449131990.0001155145776010.1720246680570.03354431411570.16489741378929.7770.95535.267
21.98516395454-0.8677759626330.6425898474741.92427937544-0.6207818290541.213342060680.02455120128880.0973248251656-0.14383592818-0.181487870274-0.02713704679850.02462773572960.1297716150660.0774479724140.00451709775870.2250083136150.04072725018210.04450599879290.1811162788580.01204428111110.18620872046335.196-14.9969.005
31.961214114840.3205009985580.6767694295881.503307830690.5107671290281.136342984720.0240351922692-0.0893896579845-0.1026480751590.121499199979-0.080248522907-0.1211149716240.3168418490670.206872157850.04213106183630.1899176703550.08347198073980.01483617985080.2166285382170.05916426702610.18657082915538.269-17.03827.33
41.792663476160.1965836119220.3930169626576.507445154370.2621701586560.108592021927-0.0934456336087-0.390209914759-0.06523796978170.06798504956650.00459216513614-0.9346258374830.1612139626450.8501807267260.06344421839580.1974581685110.1170752052510.03178664425430.563030386340.01201411771010.36858019936151.865-11.95321.165
51.23674402076-0.366493167176-0.09278043148231.32184143641-0.2960857554541.212304707480.00889890604124-0.03562491629950.134254819662-0.0151985060144-0.0207313921792-0.156066756607-0.04534763034530.2237674288040.01731325391670.124302766278-0.0140316818181-0.001924869667080.1859144925220.02192950655990.21693605026137.2125.10224.819
69.040460405533.582551839654.344178150977.929379146743.373865341931.99988951048-0.09168458849290.4154308313270.9297984904090.319344220493-0.3747216483620.3518109954030.3723553268160.1639081802190.4095202860160.2640698662330.1032314914080.03552183820240.1990909626330.01457853895520.25065450536928.941-10.7817.63
73.68443953275-1.36193465647-2.797620397451.350299656681.786530349132.74280289831-0.227883329722-0.152336701241-0.2511306360460.521830759243-0.1216531713160.01670504976080.430288048513-0.03080242945850.2772498592760.269873328962-0.002483620590660.005635010613870.173629245186-0.002425199896680.25983776409713.637-8.12338.713
80.880543162643-0.8383450730210.4612323823951.82289889929-0.8270674648450.5389547668070.0314618078328-0.0112882698370.007210742963360.0342191147883-0.02097642312750.115319237035-0.0725191128569-0.0411708825236-0.0183506800370.1472901813520.00107936349221-0.001111108997810.130082813158-0.01797616770510.1732418332992.74512.31627.57
92.38938823663-0.468254584208-0.1457190676961.985788446350.09959955278131.000639526630.1434176335530.233853299949-0.00984243305636-0.379220945994-0.145452244947-0.107021690231-0.06219465841510.0393607804653-0.00014196001930.2650066563330.07157544385790.02504958466820.2010826637740.01412272384260.1546211145763.73217.8416.522
103.71435423417-1.88602778805-1.547071295953.698236716632.127844505222.559843133880.3246491389510.249272550861-0.128350178551-0.595147855986-0.199494864759-0.335564670584-0.04993000521260.0641558620234-0.09804272446040.275450454150.05347499780640.03545517107570.1807605351930.02896767955740.2065957472699.6616.0396.404
113.29976241653-0.540861965208-1.292956029736.42865576346-2.080981095555.790452208460.1567559407740.1316152797820.543750867838-0.2295634165530.105774969632-0.139374212576-0.3671389625290.0216630747898-0.2515897581030.149044659190.0153207646441-0.003958097423120.133921311207-0.008394477556050.2259379415983.86530.09521.136
122.76532337158-0.115820966019-0.1497500175251.37295967687-0.1083960243751.574543929610.03336765299210.005070403431140.05535296250010.0100448342970.006627514830120.171753916199-0.0474045499543-0.164900586353-0.03567218112350.1615913960070.03078740854040.01236640375090.1192139558450.01128581187710.187581003949-3.29117.35326.174
132.13081696363-0.143417071826-0.7290639296671.60687176469-0.6732257212232.245609135870.02438315765790.137961273829-0.0768840199946-0.1820029393830.03399110142350.2405706249860.105547126264-0.253489568076-0.0401492571250.1364779660350.0031636355902-0.01949536500160.109149584749-0.01407820663810.216739845687-4.0914.01321.806
141.41880862832-0.816907979875-1.057730715652.48638969155-0.1929985984952.77855904334-0.01903396840880.163185185729-0.28403537935-0.0983951632544-0.06192374663250.2931967850890.248223263904-0.3104607637010.05421115467050.150088970025-0.000145502640132-0.01442625463980.126536314914-0.01150089052180.2004665747513.186-2.46625.503
152.18484940877-2.10427294821-2.944763985473.050973011224.011776213926.69891688819-0.00103369010303-0.0788278209965-0.04449150550.114087586231-0.04143147566760.005008238015570.0503893634128-0.1109504141780.1311651818480.163397259929-0.0120231361551-0.0008991827589920.1356516393020.02064123100420.24485114953310.083-7.51433.385
161.587088541193.36858598828-2.808335020761.99993306574-3.739433473016.6881780897-0.00925619136096-0.0441685831203-0.073865403440.0277057653921-0.0323137033161-0.01178448435840.0455921085042-0.04549197492730.1251101613350.148695884263-0.043445611420.3157096368850.417091508031-0.09001629062680.21958558828910.54314.62817.986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:46 )A2 - 46
2X-RAY DIFFRACTION2( CHAIN A AND RESID 47:161 )A47 - 161
3X-RAY DIFFRACTION3( CHAIN A AND RESID 162:217 )A162 - 217
4X-RAY DIFFRACTION4( CHAIN A AND RESID 218:237 )A218 - 237
5X-RAY DIFFRACTION5( CHAIN A AND RESID 238:352 )A238 - 352
6X-RAY DIFFRACTION6( CHAIN A AND RESID 413:413 )A413
7X-RAY DIFFRACTION7( CHAIN B AND RESID -4:14 )B-4 - 14
8X-RAY DIFFRACTION8( CHAIN B AND RESID 15:70 )B15 - 70
9X-RAY DIFFRACTION9( CHAIN B AND RESID 71:114 )B71 - 114
10X-RAY DIFFRACTION10( CHAIN B AND RESID 115:149 )B115 - 149
11X-RAY DIFFRACTION11( CHAIN B AND RESID 150:174 )B150 - 174
12X-RAY DIFFRACTION12( CHAIN B AND RESID 175:237 )B175 - 237
13X-RAY DIFFRACTION13( CHAIN B AND RESID 238:288 )B238 - 288
14X-RAY DIFFRACTION14( CHAIN B AND RESID 289:329 )B289 - 329
15X-RAY DIFFRACTION15( CHAIN B AND RESID 330:367 )B330 - 367
16X-RAY DIFFRACTION16( CHAIN B AND RESID 409:409 )B409

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