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

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Basic information

Entry
Database: PDB / ID: 6wyw
TitleCrystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Asp at pH 4.5
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: 2.13 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)145,3168
Polymers144,7844
Non-polymers5324
Water15,673870
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16550 Å2
ΔGint-75 kcal/mol
Surface area36820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.728, 80.728, 176.401
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) / Variant (production host): RIPL / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 870 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M sodium acetate, pH 4.5, 25% 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: Aug 9, 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
ReflectionResolution: 2.13→39.4 Å / Num. obs: 71715 / % possible obs: 97.2 % / Redundancy: 5.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.028 / Net I/σ(I): 27.3
Reflection shellResolution: 2.13→2.18 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 1789 / CC1/2: 0.941 / Rpim(I) all: 0.127 / % possible all: 48.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PGA

4pga


Resolution: 2.13→39.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.364 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 2783 3.9 %RANDOM
Rwork0.1418 ---
obs0.144 68787 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.13 Å2 / Biso mean: 25.673 Å2 / Biso min: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.13→39.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9593 0 36 870 10499
Biso mean--22.76 32.97 -
Num. residues----1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0139763
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179295
X-RAY DIFFRACTIONr_angle_refined_deg2.1831.6313212
X-RAY DIFFRACTIONr_angle_other_deg1.5621.58221553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42851265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41523.689469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.092151718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9771552
X-RAY DIFFRACTIONr_chiral_restr0.1130.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211029
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021859
LS refinement shellResolution: 2.13→2.184 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.239 185 -
Rwork0.175 4920 -
obs--95.9 %

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