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- PDB-8x6z: 1-naphthylamine GS from Pseudomonas sp. JS3066 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8x6z
Title1-naphthylamine GS from Pseudomonas sp. JS3066
ComponentsGlutamine synthetase
KeywordsLIGASE / glutamine synthetase / 1-naphthylamine glutamine synthetase
Function / homology:
Function and homology information
Biological speciesPseudomonas (RNA similarity group I)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsZhou, N.Y. / Zhang, S.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Elife / Year: 2024
Title: Discovery of the 1-naphthylamine biodegradation pathway reveals a broad-substrate-spectrum enzyme catalyzing 1-naphthylamine glutamylation.
Authors: Zhang, S.T. / Deng, S.K. / Li, T. / Maloney, M.E. / Li, D.F. / Spain, J.C. / Zhou, N.Y.
History
DepositionNov 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,15016
Polymers341,6006
Non-polymers54910
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.635, 140.141, 218.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glutamine synthetase


Mass: 56933.402 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Gene: HBO18_29070 / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 3.2 M Sodium chloride, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.95→19.98 Å / Num. obs: 79065 / % possible obs: 99.6 % / Redundancy: 7.1 % / CC1/2: 0.989 / Net I/σ(I): 9.4
Reflection shellResolution: 2.95→3.01 Å / Num. unique obs: 4423 / CC1/2: 0.762

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→19.98 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 3907 4.95 %
Rwork0.2238 --
obs0.2249 78921 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22670 0 10 729 23409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923212
X-RAY DIFFRACTIONf_angle_d1.16731488
X-RAY DIFFRACTIONf_dihedral_angle_d18.1498509
X-RAY DIFFRACTIONf_chiral_restr0.0663435
X-RAY DIFFRACTIONf_plane_restr0.0084082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.990.31511430.31312640X-RAY DIFFRACTION100
2.99-3.020.35991270.30132649X-RAY DIFFRACTION100
3.02-3.060.3261310.29112645X-RAY DIFFRACTION100
3.06-3.10.33991480.29532640X-RAY DIFFRACTION100
3.11-3.150.33171390.28912668X-RAY DIFFRACTION100
3.15-3.20.31181380.28472642X-RAY DIFFRACTION100
3.2-3.250.30911560.27142628X-RAY DIFFRACTION100
3.25-3.30.33261380.28452649X-RAY DIFFRACTION100
3.3-3.360.32181670.26872640X-RAY DIFFRACTION100
3.36-3.420.27881370.25842683X-RAY DIFFRACTION100
3.42-3.480.29051410.26332635X-RAY DIFFRACTION100
3.48-3.550.31011170.24342684X-RAY DIFFRACTION100
3.55-3.630.24411420.22962659X-RAY DIFFRACTION100
3.63-3.710.23071390.23052646X-RAY DIFFRACTION100
3.71-3.80.27211370.22272660X-RAY DIFFRACTION100
3.81-3.910.23391440.21422665X-RAY DIFFRACTION100
3.91-4.020.22271420.20742652X-RAY DIFFRACTION100
4.02-4.150.20521460.20172677X-RAY DIFFRACTION100
4.15-4.30.18071410.19182687X-RAY DIFFRACTION100
4.3-4.470.20771290.18842685X-RAY DIFFRACTION100
4.47-4.670.20331320.18222702X-RAY DIFFRACTION100
4.67-4.910.21391290.17942697X-RAY DIFFRACTION100
4.91-5.210.20641400.18562721X-RAY DIFFRACTION100
5.21-5.610.20961330.19452707X-RAY DIFFRACTION100
5.61-6.160.25891520.1992697X-RAY DIFFRACTION100
6.16-7.010.18421350.20862755X-RAY DIFFRACTION100
7.01-8.710.20571480.20152767X-RAY DIFFRACTION100
8.71-19.980.20541360.19392834X-RAY DIFFRACTION99

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