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- PDB-6v5f: L-asparaginase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 6v5f
TitleL-asparaginase from Escherichia coli
ComponentsL-asparaginase 2
KeywordsHYDROLASE / L-asparaginase / catalytic mechanism / leukemia
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
ASPARTIC ACID / SUCCINIC ACID / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSouza, T.A.C.B. / Morais, S.B. / Morini, F.S. / Meissner, G.O.
CitationJournal: To Be Published
Title: L-asparaginase from Escherichia coli: Novel insights about the behavior of flexible part of the active site
Authors: Souza, T.A.C.B. / Morais, S.B. / Morini, F.S. / Meissner, G.O.
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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)139,0108
Polymers138,5074
Non-polymers5024
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16250 Å2
ΔGint-43 kcal/mol
Surface area37910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.917, 125.435, 68.816
Angle α, β, γ (deg.)90.000, 106.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 10 or resid 45...
21(chain B and (resid 1 through 10 or resid 45...
31(chain C and (resid 1 through 10 or resid 45...
41(chain D and (resid 1 through 10 or resid 45...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 10 or resid 45...A1 - 10
121(chain A and (resid 1 through 10 or resid 45...A45 - 77
131(chain A and (resid 1 through 10 or resid 45...A79 - 184
141(chain A and (resid 1 through 10 or resid 45...A186 - 195
151(chain A and (resid 1 through 10 or resid 45...A1 - 326
161(chain A and (resid 1 through 10 or resid 45...A265 - 280
171(chain A and (resid 1 through 10 or resid 45...A289 - 325
211(chain B and (resid 1 through 10 or resid 45...B1 - 10
221(chain B and (resid 1 through 10 or resid 45...B45 - 48
231(chain B and (resid 1 through 10 or resid 45...B50 - 18
241(chain B and (resid 1 through 10 or resid 45...B1 - 326
251(chain B and (resid 1 through 10 or resid 45...B265 - 280
261(chain B and (resid 1 through 10 or resid 45...B265 - 280
271(chain B and (resid 1 through 10 or resid 45...B289 - 325
311(chain C and (resid 1 through 10 or resid 45...C1 - 10
321(chain C and (resid 1 through 10 or resid 45...C45 - 48
331(chain C and (resid 1 through 10 or resid 45...C50 - 77
341(chain C and (resid 1 through 10 or resid 45...C79 - 184
351(chain C and (resid 1 through 10 or resid 45...C186 - 280
361(chain C and (resid 1 through 10 or resid 45...C289 - 325
411(chain D and (resid 1 through 10 or resid 45...D1 - 10
421(chain D and (resid 1 through 10 or resid 45...D45 - 48
431(chain D and (resid 1 through 10 or resid 45...D50 - 77
441(chain D and (resid 1 through 10 or resid 45...D79 - 195
451(chain D and (resid 1 through 10 or resid 45...D197 - 263
461(chain D and (resid 1 through 10 or resid 45...D265 - 325

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Components

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


Mass: 34626.809 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00805, asparaginase
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 1.73 Å3/Da / Density % sol: 28.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M succinic acid pH 7.0, 15% (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4587 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 105403 / % possible obs: 97.7 % / Redundancy: 3.15 % / Biso Wilson estimate: 48.634 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.199 / Χ2: 1.496 / Net I/σ(I): 5.38
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2.413 % / Mean I/σ(I) obs: 0.33 / Num. unique obs: 16633 / CC1/2: 0.214 / Rrim(I) all: 3.401 / % possible all: 95.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.2 Å33.37 Å
Translation2.2 Å33.37 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASER2.8.0phasing
PDB_EXTRACT3.25data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eca

3eca


Resolution: 2.1→33.37 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2976 1976 3.87 %
Rwork0.2298 49025 -
obs0.2325 51001 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.13 Å2 / Biso mean: 43.543 Å2 / Biso min: 21.28 Å2
Refinement stepCycle: final / Resolution: 2.1→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9179 0 34 210 9423
Biso mean--45.45 41.28 -
Num. residues----1227
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3272X-RAY DIFFRACTION8.888TORSIONAL
12B3272X-RAY DIFFRACTION8.888TORSIONAL
13C3272X-RAY DIFFRACTION8.888TORSIONAL
14D3272X-RAY DIFFRACTION8.888TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.160.3804840.36872182226658
2.16-2.220.37211280.3553130325884
2.22-2.280.34861330.32793310344389
2.28-2.350.39631430.32173563370696
2.35-2.440.44491450.32893611375697
2.44-2.540.34351510.283837213872100
2.54-2.650.33331510.269637293880100
2.65-2.790.34271500.25237173867100
2.79-2.970.3021490.247136973846100
2.97-3.190.29891520.228537613913100
3.19-3.520.29161520.211737353887100
3.52-4.020.34661400.24343476361693
4.02-5.060.26241450.1933617376296
5.07-33.370.21121530.16583776392999

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