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- PDB-7a0u: LIGAND FREE TYPE II E. COLI ASPARAGINASE T12S/T89S DOUBLE MUTANT -

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Basic information

Entry
Database: PDB / ID: 7a0u
TitleLIGAND FREE TYPE II E. COLI ASPARAGINASE T12S/T89S DOUBLE MUTANT
ComponentsL-asparaginase 2Asparaginase
KeywordsANTITUMOR PROTEIN / LIGAND-FREE / ACUTE LYMPHOBLASTIC LEUKEMIA / 3.5.1.1 / ASPARAGINASE / AMIDOHYDROLASE
Function / homology
Function and homology information


asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding
Similarity search - Function
L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like ...L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile.
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26048715056 Å
AuthorsMaggi, M. / Scotti, C.
CitationJournal: To Be Published
Title: LIGAND FREE TYPE II E. COLI ASPARAGINASE T12S/T89S DOUBLE MUTANT
Authors: Maggi, M. / Scotti, C.
History
DepositionAug 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase 2
B: L-asparaginase 2
C: L-asparaginase 2
D: L-asparaginase 2


Theoretical massNumber of molelcules
Total (without water)142,2354
Polymers142,2354
Non-polymers00
Water12,250680
1
A: L-asparaginase 2
C: L-asparaginase 2

A: L-asparaginase 2
C: L-asparaginase 2


Theoretical massNumber of molelcules
Total (without water)142,2354
Polymers142,2354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14440 Å2
ΔGint-49 kcal/mol
Surface area42080 Å2
MethodPISA
2
B: L-asparaginase 2

B: L-asparaginase 2

D: L-asparaginase 2

D: L-asparaginase 2


Theoretical massNumber of molelcules
Total (without water)142,2354
Polymers142,2354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_666-x+1,y+1,-z+11
Buried area14390 Å2
ΔGint-49 kcal/mol
Surface area41690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.850, 61.860, 142.420
Angle α, β, γ (deg.)90.000, 117.935, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-524-

HOH

21A-577-

HOH

31B-529-

HOH

41C-497-

HOH

51D-504-

HOH

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Components

#1: Protein
L-asparaginase 2 / Asparaginase / L-asparaginase II / L-ASNase II / L-asparagine amidohydrolase II


Mass: 35558.824 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: PET101/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DELTA ansA and ansB / References: UniProt: P00805, asparaginase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 10% PEG 8000, 8% ETHYLENE GLYCOL, PH 7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.899998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2016 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.899998 Å / Relative weight: 1
ReflectionResolution: 2.26→125.83 Å / Num. obs: 53012 / % possible obs: 96.8 % / Redundancy: 2.861 % / Biso Wilson estimate: 26.1577580225 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.17 / Χ2: 0.967 / Net I/σ(I): 5.64 / Num. measured all: 151671 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.26-2.322.9060.4152.3511559402039770.6860.50898.9
2.32-2.382.8760.3532.811081390338530.7090.43398.7
2.38-2.452.8430.3153.0710586380037240.7880.38798
2.45-2.532.6980.2973.179697370335940.80.36797.1
2.53-2.612.8890.2643.710217360035360.8480.32398.2
2.61-2.72.9370.2484.0610121349634460.8740.30398.6
2.7-2.82.9270.2154.659668335633030.9040.26398.4
2.8-2.922.8820.1925.229150324131750.920.23598
2.92-3.052.7820.1685.668340307729980.9420.20797.4
3.05-3.22.7980.1486.388021296128670.9570.18296.8
3.2-3.372.9290.1357.168177285127920.9640.16597.9
3.37-3.572.9280.1287.557596266025940.9670.15797.5
3.57-3.822.8090.1197.816074255321620.9690.14784.7
3.82-4.132.6980.1048.375914234121920.9770.12993.6
4.13-4.522.9720.0969.726229216220960.9770.11896.9
4.52-5.052.9410.0929.985618197519100.9810.11296.7
5.05-5.842.8140.0969.074674175216610.9770.11894.8
5.84-7.152.8580.0919.564024147514080.9770.11295.5
7.15-10.112.9060.07610.933231117411120.9870.09394.7
10.11-125.832.7680.07611.1116946706120.9890.09591.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.43 Å125.83 Å
Translation3.43 Å125.83 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECA, 1NNS
Resolution: 2.26048715056→125.82516793 Å / SU ML: 0.283222669525 / Cross valid method: THROUGHOUT / σ(F): 1.34654533639 / Phase error: 23.7196940376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239891031969 2659 5.01792791093 %
Rwork0.171340308687 50331 -
obs0.17478859218 52990 96.9004297339 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.0203616284 Å2
Refinement stepCycle: LAST / Resolution: 2.26048715056→125.82516793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9367 0 0 680 10047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01269431507899516
X-RAY DIFFRACTIONf_angle_d1.1454784213912966
X-RAY DIFFRACTIONf_chiral_restr0.06052291972821553
X-RAY DIFFRACTIONf_plane_restr0.006966977164281695
X-RAY DIFFRACTIONf_dihedral_angle_d12.27312226135734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2605-2.30160.2881868848141500.2528164253252686X-RAY DIFFRACTION98.9532449407
2.3016-2.34590.3240861304911240.2238693222562675X-RAY DIFFRACTION98.8696573649
2.3459-2.39380.3021767242131430.2240223889862686X-RAY DIFFRACTION98.5714285714
2.3938-2.44580.2796481280671550.210185243752644X-RAY DIFFRACTION98.1072555205
2.4458-2.50270.2634653686541400.2042876476522646X-RAY DIFFRACTION97.6858345021
2.5027-2.56530.2798789007041490.1924514646122633X-RAY DIFFRACTION97.0690858339
2.5653-2.63470.2880732056461400.1868518218682709X-RAY DIFFRACTION99.0611961057
2.6347-2.71220.271576399421330.1914598528922675X-RAY DIFFRACTION98.4917572781
2.7122-2.79970.2562284245811360.1830697924172674X-RAY DIFFRACTION98.5619081024
2.7997-2.89980.2650108596821520.1913015853262668X-RAY DIFFRACTION98.3263598326
2.8998-3.01590.275811358931500.1717987506912653X-RAY DIFFRACTION97.6655052265
3.0159-3.15320.2577061098941450.1743922784992632X-RAY DIFFRACTION96.1898164184
3.1532-3.31950.2139391800021530.1707455587262653X-RAY DIFFRACTION98.2837127846
3.3195-3.52740.2629561350351320.1624094310192676X-RAY DIFFRACTION97.9420997558
3.5274-3.79980.206973203008990.1600231962442389X-RAY DIFFRACTION86.2690707351
3.7998-4.18220.1955085854961300.1460857743542609X-RAY DIFFRACTION94.4482758621
4.1822-4.78740.1912854143621620.1242375185492685X-RAY DIFFRACTION97.3000683527
4.7874-6.03170.2250056211781310.1460282723342634X-RAY DIFFRACTION95.3119613926
6.0317-1250.1956991269031350.1670383506882704X-RAY DIFFRACTION94.3816489362
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)
13.458622506760.3895329698260.2755378740431.844768898090.1813414364083.31404463766-0.267148931650.3696546384270.167579371833-0.2105074497410.221071122637-0.123747840956-0.2518754557420.3198706784560.04609207949770.402191802112-0.0228990312960.03658726857820.392854435848-0.03048447115070.32558020258954.316264321245.233070572433.6217147159
21.893899113420.2790704666340.4856458446340.8204086860890.2100101075021.13783070524-0.04356507951740.0616121158187-0.129182422702-0.0388146091770.03748723544220.00219505791679-0.02461787725440.04922400517325.54456547317E-50.2867589497970.02836586281660.03354306026540.260772916881-0.005225670095750.19483529870742.930082164441.653727508242.3187689326
31.00930488165-0.4177711815530.1837072005430.75627174190.069788880960.4066265431920.003663943910040.079394575769-0.0764439075558-0.0539885486516-0.03303019799460.1338363378680.0665772325013-0.04863326462870.02826540587790.2719829914360.01559970417510.004215494020120.234850026309-0.01854631068570.18458662187530.303332102946.240166219651.2738125308
42.99274873004-0.2384586218520.9666465141711.79380034086-0.3877603402741.085631884280.11150923893-0.165768821411-0.02663408885760.14036254149-0.1024252671090.2801714416150.119274652119-0.255980398718-0.007247669884910.30174126234-0.03968847580650.02518013373580.305270601861-0.0483848172650.24300667679318.709609871343.710831677255.539060775
51.577162056410.026451719177-1.020917982392.771192918270.9845362308491.096692031280.09157933340930.3568505234580.196817986651-0.78411176833-0.368274040504-0.1383979461140.1052177410170.2202373702750.2558048108560.281144449786-0.0255720548426-0.05336306095340.2767079227290.04918906678150.36379742896516.869884512244.5526013239-21.6689854893
61.11260156527-0.4339323727110.2413865542050.855549766718-0.526611829090.618532601633-0.02482960557070.3456023464540.125148820618-0.3406629825580.0290933981406-0.05064268481410.0587343582847-0.0747328618963-0.02793460304110.368025082652-0.03764049922830.009695152332770.3363102048930.07696256305690.24792922867822.240754481539.5643132388-16.9351136599
71.83304248051-0.1359748918831.090020182340.2495516581550.3590994634991.50889887009-0.2174842985340.3011879594020.2086630798240.0594453197819-0.0516331264595-0.0884034113582-0.2367698262860.2262676662370.2615925702350.164390171132-0.02120254131850.01615525173080.2496403292480.0737882255480.27551472167323.357112118845.6367365082-8.66850289942
81.119614600160.7641666897390.5466448000070.619019398002-0.002258589414521.70301748658-0.03283594164760.05280792135-0.0648619712247-0.01906998448-0.0356344620349-0.353987147036-0.07148102426550.008516850476850.03903858672750.2014096709950.009650906296290.03520160959220.2446202235220.01341032993290.24880905252616.718954279438.3168380547-8.75321702127
90.457731449149-0.146354449249-0.04524629745410.637278165987-0.1689571615730.490694686488-0.02138572763370.05510929889010.066941268397-0.00071432293575-0.00684646413565-0.0245302035766-0.1210224366640.001182626297230.03324315695530.164749644108-0.01384042054680.005166426169380.2061110551830.01179095699180.24062612685914.157741846637.87637976910.451385506167
103.016177784530.3384014402791.682157254390.9939294181240.3922347533482.417603340450.0851080238294-0.3371415424580.07499099938580.0442606371639-0.0274859845645-0.01844832270850.13472995072-0.0441818197053-0.04788464954560.2353278016150.01007539729990.02079771597660.226537560962-0.009582483305280.22022767517217.19271135733.840199931520.7088859313
110.8982241949990.104794921880.1481404019690.837489857811-0.6952580066071.6328827569-0.0582081508005-0.02643269024030.1393527480270.0938952714201-0.0260334340375-0.210545382577-0.158700013163-0.03391841852480.07637098359210.214648086899-0.0146034081684-0.003029896003780.172930725897-0.03129573690840.30679905995117.99256356643.19735620314.4397695201
121.422111355610.6657665700721.520298940922.28293453580.8467610243591.874998568670.243398543686-0.0742293818710.05397397064020.545175465383-0.110541362491-0.2132484504510.420731080667-0.350031024275-0.1663409493360.447634546465-0.02167337399250.0220553282540.410701768312-0.0281900097610.3857841415418.852964986410.209909619179.1414248664
130.438832312537-0.09075849352310.1128471276940.6541732214170.3031779584961.19457558973-0.0485004138684-0.09930052851990.1006287112170.1052438315690.004519415033310.105571862846-0.178449374316-0.1127970548320.04533647969770.2916897010050.03944117678740.02031233613480.232206868259-0.01213945699780.23710419452324.77916247518.1660612402863.9401749798
142.296388697660.3915047135651.351710761181.107856517070.143410117973.33605240199-0.09572903079590.1247486302550.114523333446-0.2290544795280.0648496019661-0.0282045823434-0.102686283687-0.05038769838980.03582331715760.4181721871650.02645221445320.04532002861260.2296724509860.04797104813270.29571830320528.71787330022.5292636403239.543289173
150.554740451157-0.0996569992055-0.2673364731641.120129610270.2149713663271.67817606481-0.1361526631370.09841228122070.172248383327-0.355958631277-0.08227784274680.0971807673536-0.389497885415-0.1623359296380.2243455364790.397852338820.032763144202-0.04989892389940.2651838538660.008991640983540.2960213070226.832038596312.045532151845.3124169073
162.46061614834-1.5428655051-1.053200909382.139724397170.6588268265013.451872055250.191635875384-0.6880847538290.1903948736130.3847415231-0.1982255775510.489323336231-0.0798280769554-0.0021446520028-0.0333591789680.337342051272-0.04252118069530.03744470738630.447610734318-0.02597536474530.306294500518-5.4229968250611.698421949131.4934801801
171.96270377174-0.2706033447220.05195751485640.797421115836-0.06824189816150.54310904050.0295735916658-0.240812927586-0.1655410272250.159047471548-0.00168115817750.06299596582970.00773308978912-0.104473683285-0.02389396080380.247861012344-0.0276882527304-0.009601668946290.2803917215330.02096678675790.1991075892463.8266724811311.075654411223.1534840106
182.28086480697-0.21240726476-0.5581888068870.7592928307850.5357352044591.885476148810.0683196224412-0.0161068413738-0.110268256903-0.02436600107930.008692155097480.0643554465897-0.08480169899430.0415355756606-0.1213432676120.206418594481-0.0190294590998-0.01422825002250.2275191862610.02646398222790.226646818652-2.3197525128311.45054933214.0154002701
192.27546540460.0215428803198-1.03417530561.771326737571.628617491624.150319708670.1261996696360.1496125185260.268863651924-0.03029164457960.06752415055360.09842564572440.0447794054790.0885324189766-0.2028477017390.2498039517480.0385841374444-0.02173121825460.2193689317170.05119562153580.2525088448282.2889350035621.08659043138.07439633626
201.587378126280.268471364955-0.06143304819620.982264749385-0.1804855324870.5646383825590.0147064584173-0.0568889241541-0.09197681824580.0204884006306-0.0377079249728-0.1161872340050.0722666264687-0.02704135845830.01675393735790.1892247625990.0164241105105-0.01525528851270.181624931649-0.009881158583280.19276471975716.960486043114.06957320319.71885793227
212.772287010250.604045564796-0.5547008467121.86290098007-0.2323575682231.09746869778-0.04403416054630.129121304023-0.195227567241-0.02003950934310.0515792653047-0.2464415699210.1017091451120.1162272617090.01184590668980.2086393707990.0154915299727-0.02240752862270.215070103417-0.02278200916960.20416006460924.463732284113.18207149393.02298881797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 0 through 44 )
2X-RAY DIFFRACTION2chain 'B' and (resid 45 through 156 )
3X-RAY DIFFRACTION3chain 'B' and (resid 157 through 250 )
4X-RAY DIFFRACTION4chain 'B' and (resid 251 through 326 )
5X-RAY DIFFRACTION5chain 'C' and (resid -3 through 39 )
6X-RAY DIFFRACTION6chain 'C' and (resid 40 through 62 )
7X-RAY DIFFRACTION7chain 'C' and (resid 63 through 91 )
8X-RAY DIFFRACTION8chain 'C' and (resid 92 through 124 )
9X-RAY DIFFRACTION9chain 'C' and (resid 125 through 250 )
10X-RAY DIFFRACTION10chain 'C' and (resid 251 through 285 )
11X-RAY DIFFRACTION11chain 'C' and (resid 286 through 326 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 39 )
13X-RAY DIFFRACTION13chain 'D' and (resid 40 through 250 )
14X-RAY DIFFRACTION14chain 'D' and (resid 251 through 285 )
15X-RAY DIFFRACTION15chain 'D' and (resid 286 through 326 )
16X-RAY DIFFRACTION16chain 'A' and (resid 0 through 34 )
17X-RAY DIFFRACTION17chain 'A' and (resid 35 through 124 )
18X-RAY DIFFRACTION18chain 'A' and (resid 125 through 162 )
19X-RAY DIFFRACTION19chain 'A' and (resid 163 through 179 )
20X-RAY DIFFRACTION20chain 'A' and (resid 180 through 250 )
21X-RAY DIFFRACTION21chain 'A' and (resid 251 through 326 )

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