[English] 日本語
Yorodumi
- PDB-7o21: Structure of Bdellovibrio bacteriovorus Bd1075 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o21
TitleStructure of Bdellovibrio bacteriovorus Bd1075
ComponentsUncharacterized conserved
KeywordsHYDROLASE / Peptidoglycan LD-Carboxypeptidase NTF2
Function / homology
Function and homology information


peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / transferase activity
Similarity search - Function
L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / NTF2-like domain superfamily
Similarity search - Domain/homology
BROMIDE ION / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Uncharacterized conserved
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.34 Å
AuthorsLovering, A.L. / Valdivia-Delgado, M.
Funding support Chile, 1items
OrganizationGrant numberCountry
Comision Nacional Cientifica y Technologica (CONICYT)72180329 Chile
CitationJournal: Nat Commun / Year: 2022
Title: Asymmetric peptidoglycan editing generates cell curvature in Bdellovibrio predatory bacteria.
Authors: Banks, E.J. / Valdivia-Delgado, M. / Biboy, J. / Wilson, A. / Cadby, I.T. / Vollmer, W. / Lambert, C. / Lovering, A.L. / Sockett, R.E.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized conserved
B: Uncharacterized conserved
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,78731
Polymers74,6082
Non-polymers2,17929
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint11 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.189, 100.631, 62.279
Angle α, β, γ (deg.)90.000, 108.070, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized conserved


Mass: 37304.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: Bd1075
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6MNZ7

-
Non-polymers , 5 types, 532 molecules

#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1M Tris pH 7.8 0.1M KSCN 0.1M NaBr 35% peg smear broad

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.34→51.01 Å / Num. obs: 123314 / % possible obs: 95.7 % / Redundancy: 6.9 % / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Net I/σ(I): 17.5 / Num. measured all: 847565
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.34-1.365.90.43238955050.952.32185.5
3.64-51.056.31004139465210.010.02499.4

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
SOLVEphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.34→46.762 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 6091 4.96 %
Rwork0.186 116769 -
obs0.1873 122860 95.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.45 Å2 / Biso mean: 25.473 Å2 / Biso min: 11.38 Å2
Refinement stepCycle: final / Resolution: 1.34→46.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 61 502 5077
Biso mean--42.22 34.4 -
Num. residues----544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.34-1.35520.35411690.3549303174
1.3552-1.37120.36071690.3459365490
1.3712-1.38790.32571970.3254372892
1.3879-1.40550.32692040.3121386394
1.4055-1.4240.34472230.3026375794
1.424-1.44350.32162010.2939387794
1.4435-1.46410.32072090.277380595
1.4641-1.4860.27241880.2672394295
1.486-1.50920.27452060.2491380795
1.5092-1.53390.26612010.242390795
1.5339-1.56040.27931860.2342387995
1.5604-1.58880.24461930.222391095
1.5888-1.61930.25932130.2095388096
1.6193-1.65240.24212100.2029389596
1.6524-1.68830.241860.1975392696
1.6883-1.72760.22591870.1938392896
1.7276-1.77080.25472100.1944394596
1.7708-1.81870.21752210.1908389896
1.8187-1.87220.23581980.1919394697
1.8722-1.93260.2082180.1893395197
1.9326-2.00170.22071950.1812397597
2.0017-2.08180.22372080.1794399197
2.0818-2.17660.2072020.1726395398
2.1766-2.29130.22292270.1798399998
2.2913-2.43490.24082180.1757399298
2.4349-2.62290.20311960.1813403298
2.6229-2.88680.20631970.182406698
2.8868-3.30440.19492210.1782403599
3.3044-4.16280.16822200.1496407999
4.1628-46.7620.18192180.1714411899

+
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