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- PDB-7d4r: SpuA native structure -

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Basic information

Entry
Database: PDB / ID: 7d4r
TitleSpuA native structure
ComponentsProbable glutamine amidotransferase
KeywordsHYDROLASE / SpuA / gama-glutamyl-gama-aminobutyrate hydrolase / Pseudomonas aeruginosa PAO1.
Function / homology
Function and homology information


gamma-glutamyl-gamma-aminobutyrate hydrolase activity / spermidine catabolic process / polyamine catabolic process / glutamine metabolic process
Similarity search - Function
Peptidase C26, gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD-like / Peptidase C26 / Peptidase C26 / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Probable glutamine amidotransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, Y. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
National Natural Science Foundation of China (NSFC)31800627 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structure and mechanism of the gamma-glutamyl-gamma-aminobutyrate hydrolase SpuA from Pseudomonas aeruginosa.
Authors: Chen, Y. / Jia, H. / Zhang, J. / Liang, Y. / Liu, R. / Zhang, Q. / Bartlam, M.
History
DepositionSep 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 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

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Assembly

Deposited unit
A: Probable glutamine amidotransferase
B: Probable glutamine amidotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0614
Polymers53,0122
Non-polymers492
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-47 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.769, 72.625, 63.774
Angle α, β, γ (deg.)90.000, 98.986, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Probable glutamine amidotransferase


Mass: 26506.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: spuA, PA0297 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I6J4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.8
Details: 0.1 M BIS-Tris pH 6.8, 30% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 55668 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.16 Å2 / Rpim(I) all: 0.05 / Net I/σ(I): 18.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.9 % / Num. unique obs: 2361 / Rpim(I) all: 0.221 / % possible all: 83.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VPI

2vpi


Resolution: 1.6→40.96 Å / SU ML: 0.2042 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.7885
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2314 1997 3.59 %
Rwork0.1907 53616 -
obs0.1922 55613 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.45 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 2 343 3704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00973438
X-RAY DIFFRACTIONf_angle_d1.04594679
X-RAY DIFFRACTIONf_chiral_restr0.0587525
X-RAY DIFFRACTIONf_plane_restr0.0072621
X-RAY DIFFRACTIONf_dihedral_angle_d6.1261474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.33441220.28573271X-RAY DIFFRACTION83.35
1.64-1.680.31411340.28313612X-RAY DIFFRACTION93.84
1.68-1.730.33841400.27143794X-RAY DIFFRACTION97.84
1.73-1.790.29261460.25263891X-RAY DIFFRACTION99.43
1.79-1.850.24971440.22913869X-RAY DIFFRACTION99.5
1.85-1.930.29561450.22393899X-RAY DIFFRACTION99.63
1.93-2.020.23131440.20713871X-RAY DIFFRACTION99.68
2.02-2.120.24981460.20553904X-RAY DIFFRACTION99.8
2.12-2.260.23631450.19893884X-RAY DIFFRACTION99.58
2.26-2.430.22361450.18683906X-RAY DIFFRACTION99.88
2.43-2.670.22321460.18653921X-RAY DIFFRACTION99.78
2.67-3.060.2351450.19223901X-RAY DIFFRACTION99.7
3.06-3.850.22851460.17293917X-RAY DIFFRACTION99.75
3.86-40.960.18731490.15813976X-RAY DIFFRACTION99.25

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