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- PDB-6wz6: Complex of mutant (K173M) of Pseudomonas 7A Glutaminase-Asparagin... -

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Basic information

Entry
Database: PDB / ID: 6wz6
TitleComplex of mutant (K173M) of Pseudomonas 7A Glutaminase-Asparaginase with L-Glu at pH 5. Covalent acyl-enzyme intermediate
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
GLUTAMIC ACID / Glutaminase-asparaginase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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
Revision 1.3Oct 30, 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: Glutaminase-asparaginase
B: Glutaminase-asparaginase
C: Glutaminase-asparaginase
D: Glutaminase-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,56711
Polymers144,7924
Non-polymers7757
Water32,1211783
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19090 Å2
ΔGint-66 kcal/mol
Surface area37570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.630, 130.463, 81.414
Angle α, β, γ (deg.)90.000, 118.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36198.008 Da / Num. of mol.: 4 / Fragment: UNP residues 26-362 / Mutation: K173M
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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 1783 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M sodium malonate, 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: 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: 1.15→34.51 Å / Num. obs: 470476 / % possible obs: 93 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Net I/σ(I): 27.1
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 13625 / CC1/2: 0.808 / Rpim(I) all: 0.26 / % possible all: 53.9

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Processing

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

4pga


Resolution: 1.15→34.51 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.986 / SU B: 0.78 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1201 3771 0.8 %RANDOM
Rwork0.0998 ---
obs0.1 444163 88.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 254.23 Å2 / Biso mean: 18.344 Å2 / Biso min: 10.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å2-0.09 Å2
2---0.55 Å20 Å2
3---0.9 Å2
Refinement stepCycle: final / Resolution: 1.15→34.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9928 0 48 1795 11771
Biso mean--20.05 34.44 -
Num. residues----1320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01310404
X-RAY DIFFRACTIONr_bond_other_d0.0050.0179886
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.63414122
X-RAY DIFFRACTIONr_angle_other_deg1.6811.58123013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46151372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18523.901505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4151864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0091554
X-RAY DIFFRACTIONr_chiral_restr0.1290.21409
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211816
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021978
X-RAY DIFFRACTIONr_rigid_bond_restr12.618320290
LS refinement shellResolution: 1.15→1.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 56 -
Rwork0.426 9593 -
all-9649 -
obs--25.73 %

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