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- PDB-7drp: Structure of ATP-grasp ligase PsnB complexed with phosphomimetic ... -

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Basic information

Entry
Database: PDB / ID: 7drp
TitleStructure of ATP-grasp ligase PsnB complexed with phosphomimetic variant of minimal precursor, Mg, and ADP
Components
  • ATP-grasp domain-containing protein
  • PsnA214-38, Precursor peptide, phospho-mimic
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: 2.98 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
F: PsnA214-38, Precursor peptide, phospho-mimic
E: PsnA214-38, Precursor peptide, phospho-mimic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,36218
Polymers153,4596
Non-polymers1,90312
Water21612
1
A: ATP-grasp domain-containing protein
B: ATP-grasp domain-containing protein
E: PsnA214-38, Precursor peptide, phospho-mimic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6819
Polymers76,7303
Non-polymers9526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-78 kcal/mol
Surface area26000 Å2
MethodPISA
2
C: ATP-grasp domain-containing protein
D: ATP-grasp domain-containing protein
F: PsnA214-38, Precursor peptide, phospho-mimic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6819
Polymers76,7303
Non-polymers9526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-79 kcal/mol
Surface area26570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.587, 91.656, 98.198
Angle α, β, γ (deg.)90.000, 101.310, 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, phospho-mimic


Mass: 2681.874 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.: 4 / 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.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / 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: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.98→33.19 Å / Num. obs: 31794 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 67.41 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.044 / Rrim(I) all: 0.118 / Χ2: 2.372 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.057.30.57915830.8910.230.6241.71100
3.05-3.117.30.52815520.8980.210.5681.802100
3.11-3.177.30.43416000.9370.1730.4681.808100
3.17-3.237.30.36615650.9590.1460.3941.86100
3.23-3.37.30.31715900.9670.1260.3411.864100
3.3-3.387.30.27115750.9750.1070.2912.018100
3.38-3.467.20.23215750.980.0920.252.043100
3.46-3.567.30.19515870.9870.0770.212.154100
3.56-3.667.20.16416100.9890.0650.1772.22100
3.66-3.787.20.14415790.990.0570.1552.411100
3.78-3.917.20.13615730.9920.0540.1472.376100
3.91-4.077.20.11915870.9940.0470.1282.502100
4.07-4.267.20.10515820.9940.0420.1132.528100
4.26-4.487.20.09215910.9940.0370.12.926100
4.48-4.767.20.08516010.9960.0340.0912.674100
4.76-5.137.20.08115790.9960.0330.0882.631100
5.13-5.647.10.08116120.9960.0320.0882.547100
5.64-6.467.10.08215980.9950.0330.0892.498100
6.46-8.1370.06516150.9970.0260.072.731100
8.13-33.196.60.06216400.9960.0260.0684.30498.7

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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: 2.98→33.19 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 1558 4.9 %
Rwork0.2065 30206 -
obs0.2067 31764 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.23 Å2 / Biso mean: 69.16 Å2 / Biso min: 35.28 Å2
Refinement stepCycle: final / Resolution: 2.98→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9355 0 116 12 9483
Biso mean--67.11 63.47 -
Num. residues----1247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.98-3.070.26951290.31152451258089
3.07-3.180.32981330.295327432876100
3.18-3.310.2641470.291227682915100
3.31-3.460.23051330.257227712904100
3.46-3.640.22941520.233527462898100
3.64-3.870.22661330.215827742907100
3.87-4.170.19491250.19227822907100
4.17-4.590.17751520.173327662918100
4.59-5.250.17041520.175927632915100
5.25-6.60.20141640.206427882952100
6.61-33.190.20061380.167728542992100

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