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- PDB-9qcz: Crystal structure of Rhizobium etli L-asparaginase ReAV K263A mutant -

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Basic information

Entry
Database: PDB / ID: 9qcz
TitleCrystal structure of Rhizobium etli L-asparaginase ReAV K263A mutant
ComponentsL-asparaginase II
KeywordsHYDROLASE / Rhizobium etli / amidohydrolases / L-asparaginases / site-directed mutagenesis
Function / homologyL-asparaginase II / L-asparaginase II / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / L-asparaginase II
Function and homology information
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: To Be Published
Title: Crystal structure of Rhizobium etli L-asparaginase ReAV K263A mutant
Authors: Pokrywka, K. / Grzechowiak, M. / 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

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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)161,94753
Polymers158,0514
Non-polymers3,89649
Water27,9051549
1
A: L-asparaginase II
B: L-asparaginase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,76524
Polymers79,0262
Non-polymers1,74022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-145 kcal/mol
Surface area25480 Å2
2
C: L-asparaginase II
D: L-asparaginase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,18229
Polymers79,0262
Non-polymers2,15627
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-150 kcal/mol
Surface area25420 Å2
Unit cell
Length a, b, c (Å)77.887, 91.507, 114.338
Angle α, β, γ (deg.)90.000, 97.080, 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


Mass: 39512.766 Da / Num. of mol.: 4 / Mutation: K263A
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

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Non-polymers , 9 types, 1598 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1549 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 22% PEG 3350, 0.2 M Li2SO4, 0.1 M Tris pH 8.5

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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: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.6→91.51 Å / Num. obs: 207205 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.78 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.114 / Net I/σ(I): 7.98
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 32544 / CC1/2: 0.629 / Rrim(I) all: 0.952

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.69 Å / SU ML: 0.1732 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.4469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1919 1034 0.5 %
Rwork0.1604 206066 -
obs0.1605 207100 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.94 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10348 0 224 1549 12121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012211092
X-RAY DIFFRACTIONf_angle_d1.050615020
X-RAY DIFFRACTIONf_chiral_restr0.07111657
X-RAY DIFFRACTIONf_plane_restr0.0111980
X-RAY DIFFRACTIONf_dihedral_angle_d13.99254173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.690.2881430.262128427X-RAY DIFFRACTION96.22
1.69-1.790.25531480.226129547X-RAY DIFFRACTION99.87
1.79-1.930.25311480.192629470X-RAY DIFFRACTION99.76
1.93-2.120.20371490.157529548X-RAY DIFFRACTION99.8
2.12-2.430.17911480.148629572X-RAY DIFFRACTION99.74
2.43-3.060.21691490.153929658X-RAY DIFFRACTION99.9
3.06-48.690.14881490.138529844X-RAY DIFFRACTION99.4
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.07978304744-6.30752736366-2.447181939235.766604531481.928602896271.35141559242-0.282192103723-0.364251068456-0.1292646494290.3019470131030.2592171632130.1074275385910.1096318591450.1405857600950.03930890206590.15358023202-0.007034176225350.04031325488160.1407398566130.004254823894810.1661197965046.2448905352941.346044460963.2144188382
21.67590156229-0.9736929438970.8259371596712.380686358380.5366171370131.938607704120.00248841188977-0.183468940956-0.02994870540650.2484572699050.03470674054830.218848365648-0.113566316881-0.23119707965-0.03258600037910.1378442781420.02183434247620.03872856521630.1073663641830.0007299877787270.137049545241-3.8486554377954.478386023967.1973268617
31.06698961071-0.196629990546-0.2899522742920.546931179550.4832447980531.645873787170.04201719902020.06526498451860.0377702695202-0.074482709314-0.0632317649969-0.011528426933-0.0646211612226-0.0461496704940.02462221107040.1319610887040.01776355547160.02263520342090.08119070685220.009210306838590.121536180993-5.3087474900564.868451815940.3563945407
42.58387175608-1.03385375883-1.078469718392.450629690221.138917728732.593757846270.09840641188380.089487992469-0.163029026233-0.16822485758-0.0661149739431-0.1921298504320.1364071690630.215505056712-0.0651076143120.1730270725070.03364436251950.02214420039830.1356869126040.004749875416030.149524747162.8507357833660.874493443136.7843413209
50.441128616697-0.00418296461887-0.0741001225491.11548459010.06499539021830.687729648697-0.0008997865155330.01798057583470.0615873540068-0.0222036947793-0.01047582291890.0913321193571-0.0431344158973-0.0742210289110.01175756424430.1425817644190.01950275544980.02950914997590.1319579631010.007751918824030.175539833449-8.2213628199162.217919707352.7227285835
61.39374202778-0.775323163564-0.1569697979951.451194621790.1141097245430.453740315752-0.02211758099150.025485926948-0.1058317393710.02231976191580.02215273406670.1543409475870.0542267807074-0.07134951362950.01167099835550.141368545446-0.01077319597830.03497764790410.1214606902340.01446633070140.164745030152-3.8375886020842.013782441156.817233482
76.43052830531-6.087744831350.9767899367246.30110555266-1.163184239440.561164288224-0.320831915033-0.277995657708-0.01353887547710.3860918055560.2953595728660.0310012589816-0.0849859086660.05012076669430.01189796390020.1526798435870.002505225451880.01537170460280.135407996845-0.0002482685389530.16347370289218.44587517951.5823854363.7472506513
80.497385666423-0.314797902484-0.7626783426340.8953502230020.7925489394461.52933402046-0.0338634216423-0.0169698234756-0.0177555826596-0.05312198308080.0276664380418-0.1012376241210.05313077302810.107154907396-0.008623769965070.1325370079240.02334169629260.02471897890040.140430749480.01389833969450.1571348984632.642081194932.73132651848.1931164634
93.0073402605-1.321345978540.412825454414.19275906935-0.7364637659682.039046455060.08138892750630.108875662420.0422160802618-0.120780425812-0.08233347128710.219634679952-0.015315536063-0.120760580116-0.01056026491580.141031206550.01435766057610.03321368407030.13890093299-0.009450901495780.11980237860223.86977028829.585134482937.5970838164
100.687096937026-0.150483477748-0.3572674816411.257516141070.2731880039441.00663959576-0.0268051077533-0.104077039858-0.003819946263820.02807604958980.0670298533729-0.1488275646760.08668928080310.255091215872-0.02599556871170.1141951837530.0339068733710.01110071728320.165445823258-0.003555235319720.15059313805533.694174602537.710180403555.6587307336
113.31144397233-1.188033218661.299675163640.6718412443670.02355620852461.480394865230.02309346915390.1544509757310.09597009212230.05680538601940.0382599251695-0.06317115865010.03027561247980.068790093908-0.04003613940310.184631697178-0.03209953116190.03153634461980.1214921681520.0005671904294060.22892556131525.734492493658.121521081856.0057935892
126.685698652425.3535360566-1.913879932794.46649492804-1.38477032960.738557168756-0.2784844949790.3527716289540.0184083031362-0.2733648275590.2537496572350.004983601869830.0672476643442-0.09861768653450.04172559574190.1593992534080.003359768415760.03951785496410.1335953758760.003374496815990.154503713377-13.227176880538.8129588726-6.36117157539
130.3682871152950.1483460962151.046112865152.068858350950.3817379363352.97320217815-0.002869750938990.1648190844790.00862055024491-0.200409992680.000520402106787-0.328528131012-0.07064898771110.1659999006270.002494904904230.170950835873-0.01755661107470.06044154759740.1225120640190.01546128510560.183690013523-3.3541818932552.0956749992-10.3285348287
141.058682392060.0257669169575-0.3312220033680.402897954434-0.3437013138931.280997580060.012017654292-0.07217681434440.01817068348470.0126851578142-0.0516415313679-0.0154042613819-0.04100260698340.04491051793910.04047523128360.169840972002-0.009575907986170.02443203186250.112623921438-0.004668810414710.153352707181-2.2823407344962.985665231516.3335630093
152.841373480081.08768245491-1.00303081722.60839095713-1.042549099822.594420707390.0408344211218-0.150342485685-0.1827611214830.120207510196-0.004308799852410.3196879242910.197887061682-0.203491061758-0.07031936162810.188607143007-0.0230118708830.03907684061540.1511658399120.006167526275040.170514666662-10.201380229659.161752242519.844790765
160.950587953197-0.0992006399424-0.3188995043521.106487933920.1577534746510.8024572736330.00127945499137-0.03061632701940.0401305928917-0.02432275015270.0091564713098-0.0775907795321-0.03388091031980.00757260631017-0.009361223676640.163485005344-0.01559124854970.03653251590240.123434892981-0.0007771262809950.1696497460770.6690937896264.07011477871.73233573223
170.4568344325140.3660544299040.09854337688240.9744020418450.0006753284728640.297814955073-0.00893385017163-0.00965766307318-0.04703689086740.007038200125560.00243075900714-0.08632919198430.02376694079020.05043332380120.01251960756570.1665397715720.0116548264660.03727407823710.1412826674240.002413922634180.188492819173-1.9583388607741.47230560332.98634164346
187.460382588065.985081344160.7922730092384.801366495980.6461393161750.133436769954-0.2635895749150.385078385485-0.142576736435-0.2999851583110.267380415915-0.142569739972-0.126123889468-0.0212035060855-0.01240891920880.1658145127510.01317574102110.01204895036750.133398101985-0.001015377062890.158779330963-25.676575185548.745707858-6.96921067638
190.6194133288890.25671571457-0.5515824803020.678533283344-0.5570819376881.91987978941-0.0361649146694-0.00766175276191-0.0158698434990.0657683900297-0.02296428157030.06254771698060.0200373867403-0.1098606358040.04543943698840.135251233254-0.004518676957760.02833395063830.130507283935-0.01989567740960.164679869122-39.368402992129.41527626698.78183404903
202.754187909481.053514037420.3655754716783.967238667050.5705967171552.076625404570.144090949142-0.1369296727910.1067999490570.254620576873-0.141264856336-0.1488648127370.01144094681830.0698446653748-0.007062094310370.164454008825-0.01039180802230.03714640273290.153341387990.006615926654050.126018002148-30.554514034526.321567739119.0134012738
210.554123587609-0.0187524680097-0.1295935417110.826127687699-0.1731406331890.5151536880130.01758939146380.05351011484620.02278463249060.01674037585790.001828230243130.127504490222-0.000446648873558-0.110487295489-0.01854582658960.162098151702-0.003719367785650.02384200871350.17659516231-0.004577715378380.190312851115-40.63680576834.34676996991.25717818022
222.354510090392.146554293091.782891474492.24784727551.35092615912.012684042850.0292754312552-0.1017393203150.116953456022-0.04214329245730.04354698524940.117748297581-0.102525026904-0.00340395324831-0.06161261015060.2143820463780.0448490734290.0333968549470.1523806247960.005752740121780.253170933122-32.984651866555.49253882031.2267727165
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 28 )AA3 - 281 - 26
22chain 'A' and (resid 29 through 46 )AA29 - 4627 - 44
33chain 'A' and (resid 47 through 114 )AA47 - 11445 - 112
44chain 'A' and (resid 115 through 149 )AA115 - 149113 - 147
55chain 'A' and (resid 150 through 265 )AA150 - 265148 - 263
66chain 'A' and (resid 266 through 352 )AA266 - 352264 - 350
77chain 'B' and (resid 4 through 28 )BL4 - 281 - 25
88chain 'B' and (resid 29 through 98 )BL29 - 9826 - 95
99chain 'B' and (resid 99 through 161 )BL99 - 16196 - 158
1010chain 'B' and (resid 162 through 314 )BL162 - 314159 - 311
1111chain 'B' and (resid 315 through 353 )BL315 - 353312 - 350
1212chain 'C' and (resid 3 through 28 )CV3 - 281 - 26
1313chain 'C' and (resid 29 through 46 )CV29 - 4627 - 44
1414chain 'C' and (resid 47 through 114 )CV47 - 11445 - 112
1515chain 'C' and (resid 115 through 149 )CV115 - 149113 - 147
1616chain 'C' and (resid 150 through 237 )CV150 - 237148 - 235
1717chain 'C' and (resid 238 through 352 )CV238 - 352236 - 350
1818chain 'D' and (resid 4 through 28 )DD4 - 281 - 25
1919chain 'D' and (resid 29 through 98 )DD29 - 9826 - 95
2020chain 'D' and (resid 99 through 161 )DD99 - 16196 - 158
2121chain 'D' and (resid 162 through 314 )DD162 - 314159 - 311
2222chain 'D' and (resid 315 through 352 )DD315 - 352312 - 349

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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