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- PDB-8ece: E. coli L-asparaginase II mutant (V27T) in complex with L-Glu -

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Basic information

Entry
Database: PDB / ID: 8ece
TitleE. coli L-asparaginase II mutant (V27T) in complex with L-Glu
ComponentsL-asparaginase 2
KeywordsHYDROLASE / HYDROLYSIS OF L-ASPARAGINE
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
GLUTAMIC ACID / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsStrzelczyk, P. / Wlodawer, A. / Lubkowski, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Febs Lett. / Year: 2022
Title: The E. coli L-asparaginase V27T mutant: structural and functional characterization and comparison with theoretical predictions.
Authors: Strzelczyk, P. / Zhang, D. / Wlodawer, A. / Lubkowski, J.
History
DepositionSep 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,71513
Polymers142,8164
Non-polymers8999
Water21,3661186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15430 Å2
ΔGint-41 kcal/mol
Surface area39500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.772, 126.954, 132.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 1 - 326 / Label seq-ID: 9 - 334

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 35703.938 Da / Num. of mol.: 4 / Mutation: V27T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1186 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.14 M Sodium bromide, 14% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 105359 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.03 / Rrim(I) all: 0.111 / Net I/σ(I): 26.15
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 5199 / CC1/2: 0.76 / Rpim(I) all: 0.271 / Rrim(I) all: 0.839 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECA

3eca


Resolution: 1.86→49.44 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.781 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1915 2246 2.1 %RANDOM
Rwork0.1426 ---
obs0.1436 102581 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 129.59 Å2 / Biso mean: 35.312 Å2 / Biso min: 21.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å20 Å2
2--0.16 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.86→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9173 0 60 1186 10419
Biso mean--44.38 45.95 -
Num. residues----1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0139428
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169032
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.64812844
X-RAY DIFFRACTIONr_angle_other_deg1.5531.7220782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98851225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.30326.025395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.147151546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7131532
X-RAY DIFFRACTIONr_chiral_restr0.1210.21321
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0210874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021966
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A94480.08
12B94480.08
21A94800.06
22C94800.06
31A95160.07
32D95160.07
41B94760.07
42C94760.07
51B95770.07
52D95770.07
61C94520.07
62D94520.07
LS refinement shellResolution: 1.86→1.908 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 161 -
Rwork0.276 7058 -
all-7219 -
obs--93.6 %

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