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- PDB-7drn: Structure of ATP-grasp ligase PsnB complexed with precursor pepti... -

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Basic information

Entry
Database: PDB / ID: 7drn
TitleStructure of ATP-grasp ligase PsnB complexed with precursor peptide PsnA2 and AMPPNP
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


N-acetyl-L-aspartate-L-glutamate ligase activity / ribosomal S6-glutamic acid ligase activity / SOS response / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATP-grasp domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesPlesiocystis pacifica SIR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.56 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 / Structure summary / Category: citation / citation_author / struct
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 / _struct.title
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

Downloads & links

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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: PsnA214-38, Precursor peptide
F: PsnA214-38, Precursor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,2438
Polymers153,2316
Non-polymers1,0122
Water00
1
A: ATP-grasp domain-containing protein
B: ATP-grasp domain-containing protein
E: PsnA214-38, Precursor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1224
Polymers76,6163
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-26 kcal/mol
Surface area26290 Å2
MethodPISA
2
C: ATP-grasp domain-containing protein
D: ATP-grasp domain-containing protein
F: PsnA214-38, Precursor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1224
Polymers76,6163
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-32 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.294, 92.647, 99.571
Angle α, β, γ (deg.)90.000, 100.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37023.816 Da / Num. of mol.: 4
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.: 2 / Source method: obtained synthetically / Source: (synth.) Plesiocystis pacifica SIR-1 (bacteria) / References: UniProt: A6GH40
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: Sodium acetate, 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: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.56→50 Å / Num. obs: 19860 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 72.41 Å2 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.072 / Rrim(I) all: 0.197 / Χ2: 1.942 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.57-3.637.50.5549440.9180.2160.5951.774100
3.63-3.77.60.35510110.9370.1380.3812.071100
3.7-3.777.50.4279470.9280.1670.4592.018100
3.77-3.857.50.4610320.9390.180.4951.765100
3.85-3.937.50.4399460.960.1720.4711.768100
3.93-4.027.50.3710160.9620.1450.3971.819100
4.02-4.127.50.3179830.9690.1240.3411.736100
4.12-4.237.40.29510050.9770.1160.3181.86100
4.23-4.367.50.2359700.980.0920.2522.095100
4.36-4.57.40.1919960.9840.0750.2052.282100
4.5-4.667.40.2019900.9890.0790.2171.876100
4.66-4.847.40.1869940.990.0730.21.846100
4.84-5.067.40.179750.9880.0670.1831.767100
5.06-5.337.40.1819990.9870.0710.1951.723100
5.33-5.667.40.18210030.9850.0720.1961.712100
5.66-6.17.30.1919960.9850.0760.2061.722100
6.1-6.717.30.15610070.9890.0620.1681.785100
6.71-7.687.20.1110220.9930.0440.1181.773100
7.68-9.677.10.0659900.9970.0260.071.957100
9.67-506.60.06610340.9820.0280.0723.64298.2

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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: 3.56→32.95 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 1007 5.08 %
Rwork0.2236 18811 -
obs0.2239 19818 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.35 Å2 / Biso mean: 69.2455 Å2 / Biso min: 31.34 Å2
Refinement stepCycle: final / Resolution: 3.56→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9337 0 88 0 9425
Biso mean--68.63 --
Num. residues----1248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.56-3.740.28591320.28762547267995
3.74-3.980.27411350.275127032838100
3.98-4.280.23251560.241626582814100
4.28-4.710.23711340.215127072841100
4.71-5.390.21111630.210626882851100
5.39-6.790.22251310.226227442875100
6.79-32.950.19711560.181327642920100

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