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- PDB-7u6m: Albumin binding domain fused to a mutant of the Erwinia asparaginase -

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Basic information

Entry
Database: PDB / ID: 7u6m
TitleAlbumin binding domain fused to a mutant of the Erwinia asparaginase
ComponentsL-asparaginaseAsparaginase
KeywordsHYDROLASE / Asparaginase / Albumin binding domain
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity / cytosol
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
ASPARTIC ACID / L-asparaginase
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLavie, A. / Nguyen, H.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Haematologica / Year: 2023
Title: In vivo stabilization of a less toxic asparaginase variant leads to a durable antitumor response in acute leukemia.
Authors: Van Trimpont, M. / Schalk, A.M. / De Visser, Y. / Nguyen, H.A. / Reunes, L. / Vandemeulebroecke, K. / Peeters, E. / Su, Y. / Lee, H. / Lorenzi, P.L. / Chan, W.K. / Mondelaers, V. / De ...Authors: Van Trimpont, M. / Schalk, A.M. / De Visser, Y. / Nguyen, H.A. / Reunes, L. / Vandemeulebroecke, K. / Peeters, E. / Su, Y. / Lee, H. / Lorenzi, P.L. / Chan, W.K. / Mondelaers, V. / De Moerloose, B. / Lammens, T. / Goossens, S. / Van Vlierberghe, P. / Lavie, A.
History
DepositionMar 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase
B: L-asparaginase
C: L-asparaginase
D: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,9008
Polymers150,3684
Non-polymers5324
Water20,6811148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17380 Å2
ΔGint-43 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.150, 130.410, 155.100
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: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA1 - 32720 - 346
21TYRTYRBB1 - 32720 - 346
12THRTHRAA1 - 32620 - 345
22THRTHRCC1 - 32620 - 345
13TYRTYRAA1 - 32720 - 346
23TYRTYRDD1 - 32720 - 346
14THRTHRBB1 - 32620 - 345
24THRTHRCC1 - 32620 - 345
15TYRTYRBB1 - 32720 - 346
25TYRTYRDD1 - 32720 - 346
16THRTHRCC1 - 32620 - 345
26THRTHRDD1 - 32620 - 345

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 37591.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Gene: ansB, asn / Production host: Escherichia coli (E. coli) / References: UniProt: P06608, asparaginase
#2: Chemical
ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: ABD-ErA-(TM) at 5 mg/ml in the presence of 5 mM aspartate was crystallized using the hanging drop method at room temperature in 12-17% PEG 3350, 0.1 ammonium citrate, pH 7.0, by mixing 2 ...Details: ABD-ErA-(TM) at 5 mg/ml in the presence of 5 mM aspartate was crystallized using the hanging drop method at room temperature in 12-17% PEG 3350, 0.1 ammonium citrate, pH 7.0, by mixing 2 microliters of protein with 1 microliter of reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Jun 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 163730 / % possible obs: 99.9 % / Redundancy: 15.8 % / CC1/2: 0.996 / Net I/σ(I): 8.62
Reflection shellResolution: 1.75→1.8 Å / Num. unique obs: 25735 / CC1/2: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I48

5i48


Resolution: 1.75→19.98 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.086 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1656 8209 5 %RANDOM
Rwork0.1443 ---
obs0.1454 155521 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.13 Å2 / Biso mean: 36.384 Å2 / Biso min: 22.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å2-0 Å20 Å2
2---0.24 Å2-0 Å2
3----2.26 Å2
Refinement stepCycle: final / Resolution: 1.75→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9982 0 36 1148 11166
Biso mean--34.52 48.37 -
Num. residues----1323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01310324
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179851
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.64314040
X-RAY DIFFRACTIONr_angle_other_deg1.4961.57822755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82651351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40121.816501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.318151746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6531576
X-RAY DIFFRACTIONr_chiral_restr0.0870.21401
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022077
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A102790.06
12B102790.06
21A102390.06
22C102390.06
31A103300.05
32D103300.05
41B104000.06
42C104000.06
51B105280.05
52D105280.05
61C103000.05
62D103000.05
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 565 -
Rwork0.27 11356 -
all-11921 -
obs--99.92 %

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