[English] 日本語
Yorodumi
- PDB-6wi6: Crystal structure of plantacyclin B21AG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wi6
TitleCrystal structure of plantacyclin B21AG
ComponentsPlantacyclin B21AG
KeywordsANTIMICROBIAL PROTEIN / Circular bacteriocin / antimicrobial peptide / lactic acid bacteria
Function / homologyMALONATE ION
Function and homology information
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.8 Å
AuthorsSmith, A.T. / Gor, M.C. / Vezina, B. / McMahon, R. / King, G. / Panjikar, S. / Rehm, B. / Martin, J.
Funding support1items
OrganizationGrant numberCountry
Griffith University Postdoctoral Fellowship in Australia
Citation
Journal: Sci Rep / Year: 2020
Title: Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity.
Authors: Gor, M.C. / Vezina, B. / McMahon, R.M. / King, G.J. / Panjikar, S. / Rehm, B.H.A. / Martin, J.L. / Smith, A.T.
#1: Journal: Heliyon / Year: 2020
Title: Discovery and characterisation of circular bacteriocin plantacyclin B21AG from Lactiplantibacillus plantarum B21.
Authors: Golneshin, A. / Gor, M.C. / Williamson, N. / Vezina, B. / Van, T.T.H. / May, B.K. / Smith, A.T.
#2: Journal: Plos One / Year: 2020
Title: Cloning and functional expression of a food-grade circular bacteriocin, plantacyclin B21AG, in probiotic Lactobacillus plantarum WCFS1.
Authors: Gor, M.C. / Golneshin, A. / Van, T.T.H. / Moore, R.J. / Smith, A.T.
#3: Journal: Patent / Year: 2016
Title: Bacteriocin polypeptides and uses thereof
Authors: Golneshin, A. / Gor, M.C. / Van, T.T.H. / May, B.K. / Moore, R.J. / Smith, A.T.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / Item: _citation.details / _citation.pdbx_database_id_patent
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plantacyclin B21AG
B: Plantacyclin B21AG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4813
Polymers11,3792
Non-polymers1021
Water1,00956
1
A: Plantacyclin B21AG


Theoretical massNumber of molelcules
Total (without water)5,6901
Polymers5,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plantacyclin B21AG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7922
Polymers5,6901
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.131, 93.170, 49.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-101-

MLI

-
Components

#1: Protein Plantacyclin B21AG


Mass: 5689.649 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lactobacillus plantarum (bacteria) / Strain: B21
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.98 % / Description: Cubic shape
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.1 M sodium malonate, 0.1 M HEPES pH7.0 and 0.5% v/v JED-2003

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→46.58 Å / Num. obs: 9770 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.022 / Rrim(I) all: 0.079 / Net I/σ(I): 15.5 / Num. measured all: 128402
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8412.30.76270625730.90.2230.7952.496.7
9.01-46.5810.60.034106810110.0120.03635.699.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.8→46.58 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.187 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 993 10.2 %RANDOM
Rwork0.1693 ---
obs0.1739 8753 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.42 Å2 / Biso mean: 26.503 Å2 / Biso min: 15.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å2-0 Å2
2---0.42 Å20 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 1.8→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 7 56 865
Biso mean--21.63 39.23 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019820
X-RAY DIFFRACTIONr_bond_other_d0.0020.02836
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9591121
X-RAY DIFFRACTIONr_angle_other_deg1.05831909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.38222.516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65515118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.947152
X-RAY DIFFRACTIONr_chiral_restr0.1030.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02158
LS refinement shellResolution: 1.803→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 62 -
Rwork0.245 637 -
all-699 -
obs--98.45 %

+
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