[English] 日本語
Yorodumi
- PDB-3njw: First High Resolution Crystal Structure of a Lasso Peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3njw
TitleFirst High Resolution Crystal Structure of a Lasso Peptide
ComponentsBicyclic peptide BI-32169
KeywordsANTIMICROBIAL PROTEIN / lasso peptide / lariat / protoknot / BI-32169 / glucagon receptor antagonist / microbial peptide
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 0.86 Å
AuthorsNar, H. / Schmid, A. / Puder, C. / Potterat, O.
CitationJournal: Chemmedchem / Year: 2010
Title: High-resolution crystal structure of a lasso Peptide.
Authors: Nar, H. / Schmid, A. / Puder, C. / Potterat, O.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Atomic model / Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bicyclic peptide BI-32169


Theoretical massNumber of molelcules
Total (without water)2,0571
Polymers2,0571
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)19.465, 21.432, 29.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide Bicyclic peptide BI-32169


Mass: 2057.310 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: DSM 14996 / Production host: Streptomyces sp. (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 17.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: BI-32169 peptide in 50% DMSO/water mixture equilibrated against 20-50% MPD, 0.1-0.5M sodium phosphate or ammonium sulphate, 0.1M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 25, 2006 / Details: multilayer optics
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 0.86→8.94 Å / Num. all: 19700 / Num. obs: 19602 / % possible obs: 98.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 16
Reflection shellResolution: 0.86→0.9 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.1 / % possible all: 87.2

-
Processing

Software
NameClassification
StructureStudiodata collection
SHELXDphasing
SHELXL-97refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 0.86→8.94 Å / Num. parameters: 1443 / Num. restraintsaints: 0 / Cross valid method: THROUGHOUT / σ(F): 4
RfactorNum. reflection% reflectionSelection details
all0.1055 19602 --
obs0.0938 16628 98.7 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 124 / Occupancy sum non hydrogen: 161
Refinement stepCycle: LAST / Resolution: 0.86→8.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms144 0 0 25 169
LS refinement shellHighest resolution: 0.86 Å / Num. reflection obs: 16628

+
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