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- PDB-7r57: Escherichia coli type II Asparaginase N24S mutant in its apo form -

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Basic information

Entry
Database: PDB / ID: 7r57
TitleEscherichia coli type II Asparaginase N24S mutant in its apo form
ComponentsL-asparaginase 2
KeywordsANTITUMOR PROTEIN / 3.5.1.1 / Asparaginase / EcAII / hydrolase
Function / homology
Function and homology information


L-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, N-terminal domain / Rossmann fold - #40 / 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. ...L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsMaggi, M. / Scotti, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationNA Italy
Citation
Journal: Int J Mol Sci / Year: 2022
Title: Structural Aspects of E. coli Type II Asparaginase in Complex with Its Secondary Product L-Glutamate.
Authors: Maggi, M. / Scotti, C.
#1: Journal: Sci Rep / Year: 2017
Title: A protease-resistant Escherichia coli asparaginase with outstanding stability and enhanced anti-leukaemic activity in vitro.
Authors: Maggi, M. / Mittelman, S.D. / Parmentier, J.H. / Colombo, G. / Meli, M. / Whitmire, J.M. / Merrell, D.S. / Whitelegge, J. / Scotti, C.
History
DepositionFeb 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)141,7154
Polymers141,7154
Non-polymers00
Water20,6091144
1
A: L-asparaginase 2
B: L-asparaginase 2

A: L-asparaginase 2
B: L-asparaginase 2


Theoretical massNumber of molelcules
Total (without water)141,7154
Polymers141,7154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14430 Å2
ΔGint-52 kcal/mol
Surface area40040 Å2
MethodPISA
2
C: L-asparaginase 2
D: L-asparaginase 2

C: L-asparaginase 2
D: L-asparaginase 2


Theoretical massNumber of molelcules
Total (without water)141,7154
Polymers141,7154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14430 Å2
ΔGint-51 kcal/mol
Surface area40670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.139, 62.440, 143.409
Angle α, β, γ (deg.)90.000, 118.191, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-611-

HOH

21B-613-

HOH

31C-541-

HOH

41D-582-

HOH

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Components

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


Mass: 35428.660 Da / Num. of mol.: 4 / Mutation: N24S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ansB, b2957, JW2924 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ansA-/ansB- / References: UniProt: P00805, asparaginase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1144 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 41.93 % / Description: Prism
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) 100 mM pH 8.0, PEG 8000 5%, ETHYLENE GLYCOL 4%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07252 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07252 Å / Relative weight: 1
ReflectionResolution: 1.34→48.2 Å / Num. obs: 261282 / % possible obs: 98.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.033 / Rrim(I) all: 0.058 / Net I/σ(I): 10.1 / Num. measured all: 724964
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.34-1.392.71.02367722254960.3880.7311.2630.998.1
5.19-48.22.80.0311304446270.9970.0220.03832.897.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.58 Å47.09 Å
Translation5.58 Å47.09 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.5.31data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECA

3eca


Resolution: 1.4→47.09 Å / SU ML: 0.1514 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1845 1758 0.77 %
Rwork0.1651 227666 -
obs0.1652 229424 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.06 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9307 0 0 1144 10451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819447
X-RAY DIFFRACTIONf_angle_d0.982612880
X-RAY DIFFRACTIONf_chiral_restr0.07551558
X-RAY DIFFRACTIONf_plane_restr0.00951683
X-RAY DIFFRACTIONf_dihedral_angle_d13.90613390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.31911440.311717296X-RAY DIFFRACTION97.56
1.44-1.480.24051190.276617428X-RAY DIFFRACTION98.46
1.48-1.530.27731420.254617414X-RAY DIFFRACTION98.35
1.53-1.580.2361430.235317407X-RAY DIFFRACTION98.27
1.58-1.650.23911190.223917353X-RAY DIFFRACTION97.88
1.65-1.720.21361370.197117498X-RAY DIFFRACTION98.81
1.72-1.810.19841390.17817598X-RAY DIFFRACTION99.13
1.81-1.930.18651280.1717613X-RAY DIFFRACTION99.25
1.93-2.070.20851440.167917572X-RAY DIFFRACTION98.83
2.07-2.280.18031360.156817668X-RAY DIFFRACTION99.2
2.28-2.610.18811350.151317590X-RAY DIFFRACTION98.79
2.61-3.290.1861370.150117530X-RAY DIFFRACTION97.9
3.29-47.090.1421350.140817699X-RAY DIFFRACTION97.44

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