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- PDB-9g67: Crystal structure of Rhizobium etli L-asparaginase ReAV K138H mut... -

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Basic information

Entry
Database: PDB / ID: 9g67
TitleCrystal structure of Rhizobium etli L-asparaginase ReAV K138H 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 / : / L-asparaginase II protein
Function and homology information
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)80,55722
Polymers79,1282
Non-polymers1,42920
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-3 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.233, 91.687, 106.283
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: 39563.836 Da / Num. of mol.: 2 / Mutation: K138H
Source method: isolated from a genetically manipulated source
Details: point mutation K138H / 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, 463 molecules

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


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.89 %
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

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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: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.7→69.42 Å / Num. obs: 55231 / % possible obs: 94.4 % / Redundancy: 11.1 % / Biso Wilson estimate: 22.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.159 / Net I/σ(I): 11.4
Reflection shellResolution: 1.7→1.86 Å / Rmerge(I) obs: 1.781 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2762 / CC1/2: 0.582 / Rrim(I) all: 1.854

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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→63 Å / SU ML: 0.1641 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8062
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2158 999 1.81 %
Rwork0.1754 54197 -
obs0.1761 55196 64.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.73 Å2
Refinement stepCycle: LAST / Resolution: 1.7→63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5317 0 78 443 5838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01045558
X-RAY DIFFRACTIONf_angle_d1.07977507
X-RAY DIFFRACTIONf_chiral_restr0.0625836
X-RAY DIFFRACTIONf_plane_restr0.0111999
X-RAY DIFFRACTIONf_dihedral_angle_d14.11452056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.790.4785180.31940X-RAY DIFFRACTION8
1.79-1.90.2526790.2623177X-RAY DIFFRACTION27.16
1.9-2.050.25261030.23355891X-RAY DIFFRACTION49.9
2.05-2.250.2491400.21258607X-RAY DIFFRACTION72.58
2.25-2.580.23912060.200711317X-RAY DIFFRACTION94.97
2.58-3.250.23032170.177711975X-RAY DIFFRACTION99.88
3.25-630.18712360.146212290X-RAY DIFFRACTION99.69
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)
17.510779126334.891346548231.708745186014.068315151650.8305140878071.2204613485-0.1362055484230.2686789210360.0509876853964-0.3385156732470.0272165516380.0923639376063-0.0767406835879-0.008584547970040.0660313078580.09136665242420.008164818879590.0114877549850.125302808061-0.01903016111950.18475005764313.2696.24519.075
20.9271692069830.324241762411-0.4438109327361.7945581514-0.2903954110910.3718201477580.0724527852663-0.122857901277-0.120294181550.299511275902-0.09473256360650.2568798356850.130296602482-0.137610127282-0.02018029936070.156365287515-0.0799691041740.04811815958280.214735610181-0.05193634679710.238741408314-0.486-12.42135.307
33.125731632210.8659672525181.410365467741.73929584041.88722659582.700693339030.192393244054-0.178048597456-0.1071413581970.37186363386-0.0473247050213-0.2343312274510.1738517714280.115445405357-0.1185098260350.250629078687-0.0859795780651-0.001607681384530.2198529596840.03786270158930.2094924814078.442-15.99645.698
41.907852863320.1173658682720.5536850354590.731630065793-0.641423437570.858623775330.0181553714810.0991498571803-0.110477406162-0.042849748241-0.1410276223940.1137968582940.239510341142-0.2909284647450.02269666841260.128085242219-0.1039991380440.02186673370460.177083224732-0.08413748372380.2732616795071.181-17.17525.567
52.89406436629-0.0957253927259-1.32176699216.98001715999-0.5821058814050.659301459104-0.01858506206220.559714145519-0.227504588644-0.189046920112-0.04951269993790.9240420128160.259503010967-0.740932594498-0.04879774503050.190725106994-0.1338939982240.0685764218720.479379998183-0.05816842365310.387203548316-13.06-12.59731.668
61.077744546550.181663680895-0.3921064633961.09470668636-0.1571756068631.149940583060.109001351554-0.1244471605010.2415372381730.169777793086-0.08854064281770.27972058043-0.081355145423-0.253264214509-0.007148094106240.04661309771070.006977389107830.03548822034980.142181796605-0.06478454881690.2697128039661.6185.00528.276
73.818777945-1.348069274390.8648899127848.32560309395-6.329323389661.999980285610.1474333648030.6042695432882.28108119331-0.92958993254-0.444271416763-0.8074564937520.330290929258-0.0458918446380.2372412182640.398591769146-0.1505419456710.0609779994730.3796994754070.1452220903750.50353407619910.35-10.60635.286
82.415461675420.975016500286-0.8664687100182.16291771181-0.4987223293841.52623611942-0.1333227621670.172931632636-0.140433882864-0.2307225977770.00653773304898-0.1420368518260.05784953659470.02317807501760.0978539212810.08848124785890.0105670764848-0.005816363368790.1177454475730.005780669499690.17721209654829.8610.58516.857
91.294262776570.544569464944-0.3129361986321.24543827907-0.2185365444330.7308206793630.225966976424-0.3386180831220.1974057392450.466932930302-0.2145252469880.203538705444-0.109944314113-0.107113106454-0.01921542197710.242896140162-0.1270667596490.03638713262910.203259486734-0.05228800662390.22837148789334.91720.85441.706
101.462962918480.5997058425920.0003601809498511.298564181920.2121765432020.9419270499530.085757067051-0.0946866733632-0.0528939724360.102346863301-0.064860955363-0.27424712036-0.0130328728410.184157679536-0.01885386347190.0789051196711-0.027938918632-0.007716189091270.1346690974880.01975180126170.20902762700740.8489.26128.085
112.52817014480.819927306387-0.40563819511.58895446791-0.6438201996122.79777433739-0.1115763667930.092444311707-0.334516516722-0.143959655235-0.0326248676227-0.2549441018510.07295045040390.02563477078150.1314221934230.1588049567220.01136689671460.01205210255470.0880416378999-0.0100216275990.24613013655632.294-7.41223.643
127.65541164439-5.198398471370.1966540674484.89251105243.022954356077.31724691861-0.08500196752090.720630804287-2.31716620623-0.5465818366250.3823649095540.2603489238790.3579813007270.315192067772-0.338783578290.287009071549-0.0924781827362-0.05934584868340.526193896821-0.1829429067270.72836152591628.38514.55835.015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:28 )A2 - 28
2X-RAY DIFFRACTION2( CHAIN A AND RESID 29:97 )A29 - 97
3X-RAY DIFFRACTION3( CHAIN A AND RESID 98:161 )A98 - 161
4X-RAY DIFFRACTION4( CHAIN A AND RESID 162:216 )A162 - 216
5X-RAY DIFFRACTION5( CHAIN A AND RESID 217:237 )A217 - 237
6X-RAY DIFFRACTION6( CHAIN A AND RESID 238:352 )A238 - 352
7X-RAY DIFFRACTION7( CHAIN A AND RESID 505:505 )A505
8X-RAY DIFFRACTION8( CHAIN B AND RESID -3:46 )B-3 - 46
9X-RAY DIFFRACTION9( CHAIN B AND RESID 47:175 )B47 - 175
10X-RAY DIFFRACTION10( CHAIN B AND RESID 176:314 )B176 - 314
11X-RAY DIFFRACTION11( CHAIN B AND RESID 315:367 )B315 - 367
12X-RAY DIFFRACTION12( CHAIN B AND RESID 408:408 )B408

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