[English] 日本語
Yorodumi
- PDB-9meh: Crystal structure of the dimodular LgrA after protein ligation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9meh
TitleCrystal structure of the dimodular LgrA after protein ligation
ComponentsLinear gramicidin synthase subunit A
KeywordsBIOSYNTHETIC PROTEIN / NRPS / Condensation / Dimodule / Complex
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / antibiotic biosynthetic process / cytoplasm
Similarity search - Function
Non-ribosomal peptide synthase / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site ...Non-ribosomal peptide synthase / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Chem-J8T / Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsPistofidis, A. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-178084 Canada
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Protein ligation for the assembly and study of nonribosomal peptide synthetase megaenzymes.
Authors: Pistofidis, A. / Schmeing, T.M.
History
DepositionDec 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Linear gramicidin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,2912
Polymers206,0641
Non-polymers2271
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.235, 166.281, 178.491
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

#1: Protein Linear gramicidin synthase subunit A


Mass: 206064.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Complex was assembled by asparaginyl endopeptidase 1 (AEP1)-mediated ligation
Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Gene: lgrA / Production host: Escherichia coli (E. coli) / References: UniProt: Q70LM7
#2: Chemical ChemComp-J8T / [(3~{R})-4-azanyl-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate


Mass: 227.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14NO6P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.29 Å3/Da / Density % sol: 71.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 2% PEG 2000 MME, 0.9 M sodium succinate, 0.1 M HEPES pH 6.8, 0.1 M ammonium succinate, 0.5 mM 1-nonanoyl-2-hydroxy-sn-glycero-3-phosphocholine (09:0 lyso-PC)

-
Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2020
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 41605 / % possible obs: 99.9 % / Redundancy: 11.6 % / Biso Wilson estimate: 153.79 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.039 / Rrim(I) all: 0.135 / Χ2: 0.935 / Net I/σ(I): 18.6
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 11.3 % / Rmerge(I) obs: 2.49 / Mean I/σ(I) obs: 0.875 / Num. unique obs: 2030 / CC1/2: 0.489 / CC star: 0.811 / Rpim(I) all: 0.751 / Rrim(I) all: 2.604 / Χ2: 0.795 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-2000721data reduction
HKL-2000721data scaling
PHASER2.9.0phasing
Coot0.9.8.92model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→48.38 Å / SU ML: 0.5645 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.4905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2734 1995 4.91 %
Rwork0.2669 38605 -
obs0.2672 40600 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 195.58 Å2
Refinement stepCycle: LAST / Resolution: 3.6→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14419 0 13 0 14432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001914750
X-RAY DIFFRACTIONf_angle_d0.446320034
X-RAY DIFFRACTIONf_chiral_restr0.042241
X-RAY DIFFRACTIONf_plane_restr0.00412609
X-RAY DIFFRACTIONf_dihedral_angle_d13.73295509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.690.51691240.51412563X-RAY DIFFRACTION91.36
3.69-3.790.42911610.47842625X-RAY DIFFRACTION95.38
3.79-3.90.44611100.42532700X-RAY DIFFRACTION96.2
3.9-4.030.39351490.3882687X-RAY DIFFRACTION96.1
4.03-4.170.39521450.36192724X-RAY DIFFRACTION96.96
4.17-4.340.30891380.34692709X-RAY DIFFRACTION97.03
4.34-4.540.32891300.3152753X-RAY DIFFRACTION97.43
4.54-4.780.2851430.28212773X-RAY DIFFRACTION97.98
4.78-5.080.27861510.27282756X-RAY DIFFRACTION98.58
5.08-5.470.2741420.28582789X-RAY DIFFRACTION98.72
5.47-6.020.2731470.28092809X-RAY DIFFRACTION98.6
6.02-6.890.28671440.26822839X-RAY DIFFRACTION99.33
6.89-8.670.23381490.22782890X-RAY DIFFRACTION99.84
8.67-48.380.20251620.18272988X-RAY DIFFRACTION99.18

+
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