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- PDB-7d53: SpuA mutant - H221N with Glu -

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Basic information

Entry
Database: PDB / ID: 7d53
TitleSpuA mutant - H221N with Glu
ComponentsProbable glutamine amidotransferase
KeywordsHYDROLASE / SpuA / gama-glutamyl-gama-aminobutyrate hydrolase / glutamine amidotransferase / 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
GLUTAMIC ACID / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,61412
Polymers105,9284
Non-polymers6868
Water18,1231006
1
A: Probable glutamine amidotransferase
B: Probable glutamine amidotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3076
Polymers52,9642
Non-polymers3434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-35 kcal/mol
Surface area18780 Å2
MethodPISA
2
C: Probable glutamine amidotransferase
hetero molecules

D: Probable glutamine amidotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3076
Polymers52,9642
Non-polymers3434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area3270 Å2
ΔGint-35 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.349, 120.378, 158.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Probable glutamine amidotransferase


Mass: 26482.100 Da / Num. of mol.: 4 / Mutation: H221N
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.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1006 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris-HCl pH 8.5, 30% w/v Polyethylene glycol 4,000

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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 9, 2019
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: 120939 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.93 Å2 / Rpim(I) all: 0.04 / Net I/σ(I): 27.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5983 / Rpim(I) all: 0.359 / % possible all: 100

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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: 7D4R

7d4r


Resolution: 1.6→30.61 Å / SU ML: 0.1507 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.202 2000 1.66 %
Rwork0.1628 118801 -
obs0.1634 120801 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.86 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7430 0 4 1006 8440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01057606
X-RAY DIFFRACTIONf_angle_d1.06510360
X-RAY DIFFRACTIONf_chiral_restr0.06321148
X-RAY DIFFRACTIONf_plane_restr0.00811394
X-RAY DIFFRACTIONf_dihedral_angle_d13.62251058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.22781330.22237864X-RAY DIFFRACTION92.69
1.64-1.680.25161400.20998396X-RAY DIFFRACTION99.99
1.68-1.730.24811420.20438407X-RAY DIFFRACTION99.96
1.73-1.790.23321420.19588441X-RAY DIFFRACTION99.98
1.79-1.850.22781430.18658459X-RAY DIFFRACTION100
1.85-1.920.22771410.18618445X-RAY DIFFRACTION99.99
1.92-2.010.23111440.1758484X-RAY DIFFRACTION99.99
2.01-2.120.18151430.16468481X-RAY DIFFRACTION100
2.12-2.250.19631430.15448547X-RAY DIFFRACTION100
2.25-2.420.18051420.15688472X-RAY DIFFRACTION100
2.42-2.670.20641460.16278581X-RAY DIFFRACTION99.97
2.67-3.050.21691430.16398582X-RAY DIFFRACTION100
3.05-3.840.20781470.15318680X-RAY DIFFRACTION99.98
3.84-30.610.17691510.15078962X-RAY DIFFRACTION99.48

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