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- PDB-7r5q: Escherichia coli type II Asparaginase N24S mutant in complex with GLU -

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Basic information

Entry
Database: PDB / ID: 7r5q
TitleEscherichia coli type II Asparaginase N24S mutant in complex with GLU
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, 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
GLUTAMIC ACID / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaggi, M. / Scotti, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationDepartment of Excellence 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 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 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 / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3038
Polymers141,7154
Non-polymers5894
Water9,350519
1
A: L-asparaginase 2
C: L-asparaginase 2
hetero molecules

A: L-asparaginase 2
C: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3038
Polymers141,7154
Non-polymers5894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14730 Å2
ΔGint-54 kcal/mol
Surface area38900 Å2
MethodPISA
2
B: L-asparaginase 2
D: L-asparaginase 2
hetero molecules

B: L-asparaginase 2
D: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3038
Polymers141,7154
Non-polymers5894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14540 Å2
ΔGint-53 kcal/mol
Surface area38590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.029, 61.946, 142.564
Angle α, β, γ (deg.)90.000, 118.310, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-641-

HOH

21B-552-

HOH

31C-639-

HOH

41D-550-

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: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: HEPES pH 8.0, PEG 8000 7.5%, ETHYLENE GLYCOL 6%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 14, 2020 / Details: VERTICAL CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→47.81 Å / Num. obs: 161081 / % possible obs: 99.1 % / Redundancy: 3 % / Biso Wilson estimate: 32.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.046 / Rrim(I) all: 0.081 / Net I/σ(I): 7.8 / Num. measured all: 477220 / Scaling rejects: 1198
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
1.57-1.592.92.9252134674720.1322.0853.6080.492.9
8.59-47.8130.026303410150.9970.0180.03135.596.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDS1data reduction
Aimless0.7.4data scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECA

3eca


Resolution: 1.9→47.81 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 1138 1.25 %
Rwork0.17 89680 -
obs0.1704 90818 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.47 Å2 / Biso mean: 47.4111 Å2 / Biso min: 18.91 Å2
Refinement stepCycle: final / Resolution: 1.9→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9114 0 60 519 9693
Biso mean--57.7 40.67 -
Num. residues----1226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.990.29281430.2588111661130999
1.99-2.090.24721440.2127111531129799
2.09-2.220.2311440.19061124711391100
2.22-2.390.22731450.1865111991134499
2.39-2.630.21261390.1741111661130599
2.63-3.020.22471330.1798112591139299
3.02-3.80.19021470.1626111931134099
3.8-47.810.16151430.1482112971144097
Refinement TLS params.Method: refined / Origin x: 21.384 Å / Origin y: 31.5296 Å / Origin z: 29.0346 Å
111213212223313233
T0.2502 Å2-0.0144 Å20.0014 Å2-0.2184 Å2-0.0043 Å2--0.2159 Å2
L0.111 °2-0.1846 °20.1787 °2-0.0026 °2-0.1283 °2--0.269 °2
S-0.0091 Å °-0.0161 Å °0.0497 Å °0.0187 Å °0.0182 Å °0.0306 Å °0.042 Å °-0.0236 Å °0.0016 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 326
2X-RAY DIFFRACTION1allA327
3X-RAY DIFFRACTION1allB1 - 326
4X-RAY DIFFRACTION1allB327
5X-RAY DIFFRACTION1allC1 - 326
6X-RAY DIFFRACTION1allC327
7X-RAY DIFFRACTION1allD1 - 326
8X-RAY DIFFRACTION1allD327
9X-RAY DIFFRACTION1allS1 - 543

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