[English] 日本語
Yorodumi
- PDB-6sig: Epidermicin antimicrobial protein from Staphylococcus epidermidis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sig
TitleEpidermicin antimicrobial protein from Staphylococcus epidermidis
ComponentsEpidermicin locus structural protein
KeywordsSTRUCTURAL PROTEIN / antibiotic / helical
Function / homologyBacteriocin class II, aureocin-like / Aureocin-like type II bacteriocin / Epidermicin locus structural protein
Function and homology information
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsDerrick, J.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J021474/1 United Kingdom
CitationJournal: Iscience / Year: 2020
Title: Flowering Poration-A Synergistic Multi-Mode Antibacterial Mechanism by a Bacteriocin Fold.
Authors: Hammond, K. / Lewis, H. / Halliwell, S. / Desriac, F. / Nardone, B. / Ravi, J. / Hoogenboom, B.W. / Upton, M. / Derrick, J.P. / Ryadnov, M.G.
History
DepositionAug 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 31, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epidermicin locus structural protein
B: Epidermicin locus structural protein
C: Epidermicin locus structural protein
D: Epidermicin locus structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4096
Polymers24,2174
Non-polymers1922
Water4,125229
1
A: Epidermicin locus structural protein


Theoretical massNumber of molelcules
Total (without water)6,0541
Polymers6,0541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epidermicin locus structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1502
Polymers6,0541
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Epidermicin locus structural protein


Theoretical massNumber of molelcules
Total (without water)6,0541
Polymers6,0541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Epidermicin locus structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1502
Polymers6,0541
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.740, 99.440, 69.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-126-

HOH

21A-130-

HOH

31B-226-

HOH

41B-231-

HOH

51B-232-

HOH

61C-152-

HOH

-
Components

#1: Protein
Epidermicin locus structural protein


Mass: 6054.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus epidermidis (bacteria) / References: UniProt: H9BG66
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium Sulphate, 0.1M Sodium Acetate pH4.5, 28% PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.58→49.78 Å / Num. obs: 42997 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.209 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 18.3
Reflection shellResolution: 1.58→1.62 Å / Rmerge(I) obs: 0.649 / Num. unique obs: 3140 / Rpim(I) all: 0.308 / Rrim(I) all: 0.781

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SIF

6sif


Resolution: 1.58→49.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.203 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 2168 5 %RANDOM
Rwork0.1566 ---
obs0.1575 40821 99.85 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 146.76 Å2 / Biso mean: 23.404 Å2 / Biso min: 11 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0 Å20 Å2
2--0.11 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.58→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 10 229 1931
Biso mean--27.78 36.57 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121770
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181737
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.6192383
X-RAY DIFFRACTIONr_angle_other_deg1.5761.5884019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4655201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.88923.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54215345
X-RAY DIFFRACTIONr_chiral_restr0.0950.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
LS refinement shellResolution: 1.584→1.625 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 156 -
Rwork0.218 2978 -
all-3134 -
obs--99.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6270.1-0.07035.0147-1.74073.2388-0.0212-0.0313-0.05460.19340.10080.07780.0435-0.1003-0.07960.0710.01120.01070.01020.00510.0159-22.318-10.1116.067
23.80340.26270.67980.4944-0.34122.36360.0677-0.1824-0.04270.0351-0.0253-0.03550.02310.1061-0.04240.0286-0.0076-0.00360.0312-0.00380.0171-36.025-24.719-27.582
34.32340.5816-2.28410.5858-0.13283.58480.0745-0.20420.10850.08650.01270.0572-0.1420.1089-0.08720.04130.00070.01110.0186-0.00420.0124-55.885-21.101-19.426
40.79890.85760.0634.46382.61345.05810.00520.1422-0.0705-0.16070.1505-0.1289-0.09990.104-0.15570.0656-0.0140.00820.0359-0.0110.0241-19.014-8.721-16.531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 51
2X-RAY DIFFRACTION2B1 - 51
3X-RAY DIFFRACTION3C2 - 51
4X-RAY DIFFRACTION4D2 - 51

+
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