[English] 日本語
Yorodumi
- PDB-1o82: X-RAY STRUCTURE OF BACTERIOCIN AS-48 AT PH 4.5. SULPHATE BOUND FORM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o82
TitleX-RAY STRUCTURE OF BACTERIOCIN AS-48 AT PH 4.5. SULPHATE BOUND FORM
ComponentsPEPTIDE ANTIBIOTIC AS-48
KeywordsPEPTIDE ANTIBIOTIC / BACTERIOCIN / CATIONIC ANTIBACTERIAL PEPTIDES / MEMBRANE PERMEABILIZATION / PROTEIN CRYSTALLOGRAPHY / CYCLIC POLYPEPTIDE / PROTEIN MEMBRANE INTERACTION
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium / extracellular region / membrane
Similarity search - Function
Bacteriocin AS-48 / Bacteriocin AS-48 / Circular bacteriocin / Bacteriocin class IId cyclical uberolysin-like / Bacteriocin As-48; Chain A / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.46 Å
AuthorsSanchez-Barrena, M.J. / Martinez-Ripoll, M. / Galvez, A. / Martinez-Bueno, M. / Maqueda, M. / Cruz, V. / Albert, A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure of Bacteriocin as-48: From Soluble State to Membrane Bound State
Authors: Sanchez-Barrena, M.J. / Martinez-Ripoll, M. / Galvez, A. / Valdivia, E. / Maqueda, M. / Cruz, V. / Albert, A.
History
DepositionNov 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PEPTIDE ANTIBIOTIC AS-48
B: PEPTIDE ANTIBIOTIC AS-48
C: PEPTIDE ANTIBIOTIC AS-48
D: PEPTIDE ANTIBIOTIC AS-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,28310
Polymers28,7104
Non-polymers5726
Water5,386299
1
A: PEPTIDE ANTIBIOTIC AS-48


Theoretical massNumber of molelcules
Total (without water)7,1781
Polymers7,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEPTIDE ANTIBIOTIC AS-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3663
Polymers7,1781
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PEPTIDE ANTIBIOTIC AS-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2742
Polymers7,1781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PEPTIDE ANTIBIOTIC AS-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4664
Polymers7,1781
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.473, 83.405, 99.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6455, -0.5902, -0.4848), (-0.4593, -0.2071, 0.8638), (-0.6102, 0.7802, -0.1374)63.6992, 21.7136, 26.2744
2given(0.0415, 0.9989, 0.0226), (-0.9987, 0.0408, 0.0307), (0.0298, -0.0239, 0.9993)-0.9682, 79.6594, 0.1714
3given(-0.5288, -0.2326, 0.8162), (0.5721, 0.6127, 0.5453), (-0.6269, 0.7553, -0.1909)25.6186, 18.486, 28.5338

-
Components

#1: Protein
PEPTIDE ANTIBIOTIC AS-48 / BACTERIOCIN AS-48


Mass: 7177.538 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PEPTIDE LINK BETWEEN RESIDUES 1 AND 70 / Source: (natural) ENTEROCOCCUS FAECALIS (bacteria) / References: UniProt: Q47765
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growpH: 4.5
Details: 0.2 M AMMONIUM SULFATE, 0.1 SODIUM ACETATE TRIHYDRATE PH 4.5, 12% W/V POLYETHYLENE GLYCOL 4000AS-48 10 MG/ML
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
30.2 Mammonium sulfate1reservoir
40.1 Msodium acetate trihydrate1reservoirpH4.5
515 %(w/v)PEG40001reservoir
60.1 Msodium-Hepes1reservoirpH7.5
70.8 Mmono-sodium dihydrogen phosphate1reservoir

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.46→25.25 Å / Num. obs: 54856 / % possible obs: 94.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.1
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.4 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 1.46 Å / Lowest resolution: 25.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 94.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.4

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
CCP4phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.46→15 Å / SU B: 1.543 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.072
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2723 5 %RANDOM
Rwork0.208 ---
obs0.209 51862 94.38 %-
Displacement parametersBiso mean: 19.601 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.46→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 31 299 2346
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor Rfree: 0.2235 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.009
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.26
X-RAY DIFFRACTIONplanar_d0.005
LS refinement shell
*PLUS
Highest resolution: 1.46 Å / Lowest resolution: 1.54 Å / Rfactor Rfree: 0.34 / Rfactor Rwork: 0.29

+
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