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- PDB-7mgv: Chryseobacterium gregarium RiPP-associated ATP-grasp ligase in co... -

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Basic information

Entry
Database: PDB / ID: 7mgv
TitleChryseobacterium gregarium RiPP-associated ATP-grasp ligase in complex with ADP, and a leader and core peptide
Components
  • CdnA3 Core peptide
  • CdnA3 Leader peptide
  • CdnC
KeywordsLIGASE / Ribosomally synthesized / post-translationally modified peptide / Natural products ATP-grasp ligase / Precursor peptide / Graspetide omega-ester macrocycles macrolactone
Function / homologyADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesChryseobacterium gregarium DSM 19109 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsBewley, C.A. / Zhao, G. / Kosek, D. / Dyda, F.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic omega-Ester Macrocycles in a New Multicore RiPP Natural Product.
Authors: Zhao, G. / Kosek, D. / Liu, H.B. / Ohlemacher, S.I. / Blackburne, B. / Nikolskaya, A. / Makarova, K.S. / Sun, J. / Barry Iii, C.E. / Koonin, E.V. / Dyda, F. / Bewley, C.A.
History
DepositionApr 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CdnC
V: CdnA3 Leader peptide
U: CdnA3 Leader peptide
B: CdnC
T: CdnA3 Core peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3208
Polymers87,3745
Non-polymers9463
Water2,144119
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13750 Å2
ΔGint-80 kcal/mol
Surface area29300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.258, 80.990, 149.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CdnC


Mass: 41624.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chryseobacterium gregarium DSM 19109 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein/peptide , 2 types, 3 molecules VUT

#2: Protein/peptide CdnA3 Leader peptide


Mass: 1456.681 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Chryseobacterium gregarium DSM 19109 (bacteria)
#3: Protein/peptide CdnA3 Core peptide


Mass: 1212.242 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Chryseobacterium gregarium DSM 19109 (bacteria)

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Non-polymers , 3 types, 122 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% PEG 2000, 0.1 M bis-tris pH 6.5, 1 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.96863 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.44→30 Å / Num. obs: 29505 / % possible obs: 98.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 47.39 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Χ2: 0.894 / Net I/av σ(I): 16.8181 / Net I/σ(I): 18.5
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1438 / CC1/2: 0.687 / CC star: 0.903 / Rpim(I) all: 0.334 / Rrim(I) all: 0.652 / Χ2: 0.4 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ig9

5ig9


Resolution: 2.44→29.86 Å / SU ML: 0.3374 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.0505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256 1999 6.79 %
Rwork0.2 27451 -
obs0.2039 29450 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.86 Å2
Refinement stepCycle: LAST / Resolution: 2.44→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5726 0 60 119 5905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255902
X-RAY DIFFRACTIONf_angle_d0.60987979
X-RAY DIFFRACTIONf_chiral_restr0.0449876
X-RAY DIFFRACTIONf_plane_restr0.00341017
X-RAY DIFFRACTIONf_dihedral_angle_d8.0546779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.50.32981370.28841877X-RAY DIFFRACTION95.27
2.5-2.570.3321390.26271912X-RAY DIFFRACTION97.2
2.57-2.640.29261330.25321825X-RAY DIFFRACTION94.23
2.64-2.730.29831420.25251946X-RAY DIFFRACTION98.86
2.73-2.820.32231410.25121947X-RAY DIFFRACTION99.76
2.82-2.940.29631450.22961975X-RAY DIFFRACTION99.91
2.94-3.070.30181430.22321969X-RAY DIFFRACTION99.95
3.07-3.230.26541450.22371983X-RAY DIFFRACTION99.72
3.23-3.430.29521430.21761965X-RAY DIFFRACTION99.86
3.43-3.70.26581430.19541971X-RAY DIFFRACTION98.79
3.7-4.070.27131420.18661944X-RAY DIFFRACTION97.61
4.07-4.660.20971460.16322009X-RAY DIFFRACTION99.68
4.66-5.860.23441480.17262041X-RAY DIFFRACTION99.91
5.86-29.860.19391520.17842087X-RAY DIFFRACTION97.86

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