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- PDB-7drm: Structure of ATP-grasp ligase PsnB complexed with minimal precurs... -

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Basic information

Entry
Database: PDB / ID: 7drm
TitleStructure of ATP-grasp ligase PsnB complexed with minimal precursor, Mg, and ADP
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
ADENOSINE-5'-DIPHOSPHATE / ATP-grasp domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesPlesiocystis pacifica SIR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 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

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)154,18312
Polymers153,2316
Non-polymers9526
Water25214
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)77,0916
Polymers76,6163
Non-polymers4763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-57 kcal/mol
Surface area26010 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)77,0916
Polymers76,6163
Non-polymers4763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-59 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.432, 91.294, 100.308
Angle α, β, γ (deg.)90.000, 101.160, 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 / 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: 3.28→32.83 Å / Num. obs: 25135 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 81.45 Å2 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.055 / Rrim(I) all: 0.15 / Χ2: 4.054 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.28-3.367.50.65612700.9220.2560.7042.125100
3.36-3.427.50.64412410.90.2530.6922.267100
3.42-3.487.50.56212370.9470.2190.6042.112100
3.48-3.557.50.54512530.9590.2130.5852.424100
3.55-3.637.40.88212370.9610.3480.9492.555100
3.63-3.727.50.20812670.9410.0810.2236.957100
3.72-3.817.40.47412540.9740.1860.512.925100
3.81-3.917.50.22712160.9770.0890.2443.26100
3.91-4.037.50.25112740.980.0980.273.673100
4.03-4.167.50.20212530.9820.0790.2183.968100
4.16-4.317.50.16612290.990.0650.1783.952100
4.31-4.487.50.13812600.9910.0540.1494.742100
4.48-4.687.40.12812670.9910.050.1384.701100
4.68-4.937.40.12412440.990.0480.1334.838100
4.93-5.247.50.11812640.990.0460.1264.982100
5.24-5.647.40.11512640.9920.0450.1244.412100
5.64-6.217.40.11712740.9840.0460.1264.621100
6.21-7.17.30.09612640.990.0380.1045.445100
7.1-8.947.20.0712640.9960.0280.0755.312100
8.94-32.836.70.06313030.9950.0260.0695.94698.3

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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: 3.28→32.83 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 1201 4.88 %
Rwork0.2506 23389 -
obs0.251 24590 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.51 Å2 / Biso mean: 93.2775 Å2 / Biso min: 40.96 Å2
Refinement stepCycle: final / Resolution: 3.28→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9441 0 58 14 9513
Biso mean--77.22 70.78 -
Num. residues----1260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.28-3.410.36561380.32512481261994
3.41-3.570.34731430.36032552269597
3.57-3.750.45441300.42572358248890
3.75-3.990.26141400.28122598273897
3.99-4.30.23891250.24282626275199
4.3-4.730.21851200.201126742794100
4.73-5.410.23821340.21626822816100
5.41-6.810.24981320.241926922824100
6.81-32.830.18831390.19442726286599

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