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- PDB-6wyx: Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in c... -

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Basic information

Entry
Database: PDB / ID: 6wyx
TitleCrystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Asp at pH 5.0
ComponentsGlutaminase-asparaginase
KeywordsHYDROLASE / Amidohydrolase / Glutaminase-Asparaginase / L-Asn/L-Gln-Hydrolase
Function / homology
Function and homology information


glutamin-(asparagin-)ase / glutamin-(asparagin-)ase activity / asparagine metabolic process / asparaginase activity / glutaminase activity / periplasmic space
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 / Glutaminase-asparaginase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsStrzelczyk, P. / Zhang, D. / Wlodawer, A. / Lubkowski, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Sci Rep / Year: 2020
Title: Generalized enzymatic mechanism of catalysis by tetrameric L-asparaginases from mesophilic bacteria.
Authors: Strzelczyk, P. / Zhang, D. / Dyba, M. / Wlodawer, A. / Lubkowski, J.
History
DepositionMay 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)145,4089
Polymers144,7844
Non-polymers6255
Water22,4111244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16840 Å2
ΔGint-77 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.958, 80.958, 176.819
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Glutaminase-asparaginase / L-ASNase/L-GLNase / L-asparagine/L-glutamine amidohydrolase


Mass: 36195.992 Da / Num. of mol.: 4 / Fragment: UNP residues 26-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: ansB, PP_2453 / Plasmid: pET22b(+) / Cell (production host): Bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q88K39, glutamin-(asparagin-)ase
#2: Chemical
ChemComp-ASP / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1244 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 8% w/v Tacsimate, pH 5.0, 20% w/v PEG3350

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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: Nov 14, 2019
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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.564
11K, H, -L20.436
ReflectionResolution: 1.48→35.1 Å / Num. obs: 216530 / % possible obs: 99.8 % / Redundancy: 8.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.027 / Net I/σ(I): 27.4
Reflection shellResolution: 1.48→1.52 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10676 / CC1/2: 0.732 / Rpim(I) all: 0.349 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PGA

4pga


Resolution: 1.48→35.06 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.239 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.009 / ESU R Free: 0.009 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1199 3013 1.5 %RANDOM
Rwork0.0876 ---
obs0.0881 204714 96.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.4 Å2 / Biso mean: 16.109 Å2 / Biso min: 5.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0 Å2-0 Å2
2---1.39 Å2-0 Å2
3---2.78 Å2
Refinement stepCycle: final / Resolution: 1.48→35.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9620 0 42 1244 10906
Biso mean--15.49 29.92 -
Num. residues----1273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0199831
X-RAY DIFFRACTIONr_bond_other_d0.0020.029344
X-RAY DIFFRACTIONr_angle_refined_deg1.891.95613310
X-RAY DIFFRACTIONr_angle_other_deg1.072321681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18751279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58625.439421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.881151733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0161552
X-RAY DIFFRACTIONr_chiral_restr0.1220.21551
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211031
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021817
X-RAY DIFFRACTIONr_rigid_bond_restr3.013319175
X-RAY DIFFRACTIONr_sphericity_free27.9265809
X-RAY DIFFRACTIONr_sphericity_bonded12.245519476
LS refinement shellResolution: 1.48→1.518 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 108 -
Rwork0.161 9384 -
all-9492 -
obs--59.2 %

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