[English] 日本語
Yorodumi
- PDB-7mgv: Chryseobacterium gregarium RiPP-associated ATP-grasp ligase in co... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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)

-
Non-polymers , 3 types, 122 molecules

#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more