[English] 日本語
Yorodumi
- PDB-6lwz: Crystal structure of Laterosporulin10, bacteriocin produced by Br... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lwz
TitleCrystal structure of Laterosporulin10, bacteriocin produced by Brevibacillus sp. strain SKDU10
ComponentsBacteriocin
KeywordsTOXIN / Bacteriocin / antimicrobial peptide / Brevibacillus / Laterosporulin
Biological speciesBrevibacillus sp. SKDU10 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThakur, K.G. / Solanki, V.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: Crystal structure of Laterosporulin10, bacteriocin produced by Brevibacillus sp. strain SKDU10
Authors: Thakur, K.G. / Solanki, V.
History
DepositionFeb 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriocin
B: Bacteriocin


Theoretical massNumber of molelcules
Total (without water)12,1542
Polymers12,1542
Non-polymers00
Water25214
1
A: Bacteriocin


Theoretical massNumber of molelcules
Total (without water)6,0771
Polymers6,0771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriocin


Theoretical massNumber of molelcules
Total (without water)6,0771
Polymers6,0771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.280, 29.340, 32.150
Angle α, β, γ (deg.)110.620, 89.990, 104.940
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Bacteriocin


Mass: 6077.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Brevibacillus sp. SKDU10 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 1.57 Å3/Da / Density % sol: 21.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M calcium chloride, 0.1 M sodium cacodylate pH 5.5, 12 % PEG w/v 8000 and 3 % w/v Trimethylamine N-oxide dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→29.94 Å / Num. obs: 3487 / % possible obs: 94.1 % / Redundancy: 2.5 % / Rpim(I) all: 0.087 / Rrim(I) all: 0.141 / Rsym value: 0.111 / Net I/av σ(I): 5.8 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.322.50.4931.511914730.3840.6280.4932.190.3
2.32-2.462.50.3951.912504960.3090.5040.3952.593.6
2.46-2.632.50.3382.311054400.2650.4320.338393.6
2.63-2.842.50.25310934330.1960.3190.253.893.9
2.84-3.112.50.1445.29663790.1130.1840.144693.6
3.11-3.482.50.0927.88873520.0720.1180.0928.794.6
3.48-4.022.50.06710.67953190.0530.0860.06711.896.4
4.02-4.922.50.05910.96572660.0450.0750.05913.996
4.92-6.962.50.06110.15362130.0480.0780.06113.698.2
6.96-26.3992.40.0627.52781160.0530.0820.06214.697.1

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0218refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OZK

4ozk


Resolution: 2.2→29.94 Å / Cor.coef. Fo:Fc: 0.937 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.2579 363 -
Rwork0.2237 --
obs0.2237 3486 94.09 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.76 Å2 / Biso mean: 40.091 Å2 / Biso min: 6.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å21.21 Å20.57 Å2
2--1.47 Å21.28 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 2.2→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms842 0 0 14 856
Biso mean---35.61 -
Num. residues----106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.019868
X-RAY DIFFRACTIONr_angle_refined_deg2.1841.931172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7255104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48624.28642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7915148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.72154
X-RAY DIFFRACTIONr_chiral_restr0.090.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021662
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.327 237 -
obs--89.77 %

+
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