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- PDB-7dro: Structure of ATP-grasp ligase PsnB complexed with minimal precursor -

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Basic information

Entry
Database: PDB / ID: 7dro
TitleStructure of ATP-grasp ligase PsnB complexed with minimal precursor
Components
  • ATP-grasp domain-containing protein
  • PsnA214-38, Precursor peptide
KeywordsLIGASE / ATP-grasp ligase / RiPP / graspetide / Omega ester bond containing peptide
Function / homology
Function and homology information


ligase activity, forming carbon-nitrogen bonds / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
ATP-grasp domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesPlesiocystis pacifica SIR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsSong, I. / Yu, J. / Song, W. / Kim, S.
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Molecular mechanism underlying substrate recognition of the peptide macrocyclase PsnB.
Authors: Song, I. / Kim, Y. / Yu, J. / Go, S.Y. / Lee, H.G. / Song, W.J. / Kim, S.
History
DepositionDec 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._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: ATP-grasp domain-containing protein
B: ATP-grasp domain-containing protein
C: ATP-grasp domain-containing protein
D: ATP-grasp domain-containing protein
E: ATP-grasp domain-containing protein
F: ATP-grasp domain-containing protein
G: PsnA214-38, Precursor peptide
H: PsnA214-38, Precursor peptide
I: PsnA214-38, Precursor peptide
J: PsnA214-38, Precursor peptide


Theoretical massNumber of molelcules
Total (without water)232,41410
Polymers232,41410
Non-polymers00
Water00
1
A: ATP-grasp domain-containing protein
B: ATP-grasp domain-containing protein
G: PsnA214-38, Precursor peptide
H: PsnA214-38, Precursor peptide


Theoretical massNumber of molelcules
Total (without water)79,1834
Polymers79,1834
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATP-grasp domain-containing protein
D: ATP-grasp domain-containing protein
I: PsnA214-38, Precursor peptide


Theoretical massNumber of molelcules
Total (without water)76,6163
Polymers76,6163
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: ATP-grasp domain-containing protein
F: ATP-grasp domain-containing protein
J: PsnA214-38, Precursor peptide


Theoretical massNumber of molelcules
Total (without water)76,6163
Polymers76,6163
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.894, 146.944, 167.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ATP-grasp domain-containing protein / ATP-grasp ligase / PsnB


Mass: 37023.816 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plesiocystis pacifica SIR-1 (bacteria) / Gene: PPSIR1_03893 / Production host: Escherichia coli (E. coli) / References: UniProt: A6G4D7
#2: Protein/peptide
PsnA214-38, Precursor peptide


Mass: 2567.886 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Plesiocystis pacifica SIR-1 (bacteria) / References: UniProt: A6GH40

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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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: Tacsimate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.25→47.04 Å / Num. obs: 34587 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 80.55 Å2 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.042 / Rrim(I) all: 0.161 / Χ2: 6.643 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
3.25-3.3114.80.59416920.9460.1590.6151.729
3.31-3.3714.80.51317150.9550.1380.5311.813
3.37-3.4314.80.44917000.9590.1210.4651.868
3.43-3.514.80.39117080.9720.1050.4052.04
3.5-3.5814.80.31516880.9740.0850.3262.324
3.58-3.6614.80.25817050.9810.0690.2672.475
3.66-3.7514.90.2516950.9790.0670.2592.884
3.75-3.8514.70.23417240.980.0630.2422.677
3.85-3.9714.80.19917080.9810.0540.2073.584
3.97-4.0914.70.1817160.9840.0490.1873.652
4.09-4.2414.70.16716940.9840.0450.1734.259
4.24-4.4114.70.14417210.9780.0390.1495.598
4.41-4.6114.70.13717310.9820.0370.1427.009
4.61-4.8514.70.13117260.9840.0350.1367.41
4.85-5.1614.60.13517320.9790.0370.148.284
5.16-5.5614.50.13317380.9730.0360.1388.444
5.56-6.1114.50.13717500.9790.0370.1438.929
6.11-714.30.12517670.9780.0340.1311.331
7-8.81140.10417780.9820.0290.10817.154
8.81-47.0412.80.10718990.9780.0310.11130.601

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ig9

5ig9


Resolution: 3.25→47.04 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 1727 5.01 %
Rwork0.2555 32775 -
obs0.2558 34502 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.57 Å2 / Biso mean: 79.639 Å2 / Biso min: 30.56 Å2
Refinement stepCycle: final / Resolution: 3.25→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13250 0 0 0 13250
Num. residues----1795
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.25-3.340.37061380.3792554269294
3.34-3.450.37221420.338526912833100
3.45-3.570.27281500.303627112861100
3.57-3.720.27781510.286226972848100
3.72-3.880.31711600.285226902850100
3.89-4.090.29011120.273227592871100
4.09-4.350.22441230.248727482871100
4.35-4.680.22011200.226927372857100
4.68-5.150.23531620.231427442906100
5.15-5.90.23221350.251627792914100
5.9-7.420.29691830.261927512934100
7.42-47.040.22231510.20392914306599

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