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- PDB-7r69: Crystal structure of mutant R43D/C273S of L-Asparaginase I from Y... -

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Basic information

Entry
Database: PDB / ID: 7r69
TitleCrystal structure of mutant R43D/C273S of L-Asparaginase I from Yersinia pestis
ComponentsL-asparaginase I
KeywordsHYDROLASE / L-ASPARAGINASE
Function / homology
Function and homology information


asparaginase / asparaginase activity / amino acid metabolic process / metal ion binding / cytosol
Similarity search - Function
Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / 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 ...Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / 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
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 J. / Year: 2023
Title: The dimeric form of bacterial l-asparaginase YpAI is fully active.
Authors: Strzelczyk, P. / Zhang, D. / Alexandratos, J. / Piszczek, G. / Wlodawer, A. / Lubkowski, J.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)147,90517
Polymers147,0984
Non-polymers80713
Water18,3931021
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-33 kcal/mol
Surface area43510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.979, 162.980, 73.260
Angle α, β, γ (deg.)90.000, 110.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-asparaginase I


Mass: 36774.496 Da / Num. of mol.: 4 / Mutation: R43D, C273S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ansA, YPO2161 / Plasmid: pET22b(+) / Cell (production host): Bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: A0A3N4B0Q2, asparaginase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.2 M Ammonium chloride, 0.1 M Tris, pH 8.0, 20% (w/v) PEG 6000

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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: Jul 18, 2020
RadiationMonochromator: Double crystal - liquid nitrogen cooled Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 133825 / % possible obs: 98.5 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.032 / Net I/σ(I): 21.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6515 / CC1/2: 0.78 / Rpim(I) all: 0.313 / % possible all: 95.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NTX

3ntx


Resolution: 1.8→41.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.023 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 1882 1.4 %RANDOM
Rwork0.1669 ---
obs0.1673 128764 96.09 %-
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: 117.3 Å2 / Biso mean: 37.483 Å2 / Biso min: 15.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å2-0.09 Å2
2---0.01 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.8→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9534 0 52 1021 10607
Biso mean--53.58 46.95 -
Num. residues----1242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0139840
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179124
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.63613370
X-RAY DIFFRACTIONr_angle_other_deg1.511.56421211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33851231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56123.776482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.072151603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8531542
X-RAY DIFFRACTIONr_chiral_restr0.1020.21331
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0210966
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021876
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.263 101 -
Rwork0.236 7358 -
obs--74.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67250.17790.17080.30150.0880.19020.0560.00610.03440.0284-0.01990.06140.0122-0.0097-0.0360.14790.01070.01810.1803-0.02640.2603-11.0041104.14776.146
20.5752-0.0406-0.01520.171-0.31210.59320.0209-0.1480.0451-0.0372-0.04360.00140.04190.10470.02280.1375-0.00180.00070.2537-0.01790.218416.04899.043319.1791
30.17790.1546-0.06740.53040.01141.06190.1206-0.0755-0.12240.0062-0.0931-0.0632-0.1206-0.0135-0.02750.213-0.0199-0.01690.15260.04540.2221-9.757956.747611.9881
40.89090.85630.0081.31820.13140.06140.3329-0.335-0.06340.2656-0.29420.0237-0.0564-0.019-0.03870.3557-0.28330.0470.37570.04010.084-13.68867.962240.3665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 337
2X-RAY DIFFRACTION2B3 - 337
3X-RAY DIFFRACTION3C2 - 337
4X-RAY DIFFRACTION4D4 - 337

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