[English] 日本語
Yorodumi
- PDB-6gq5: Crystal Structure of the PSMalpha3 Peptide Mutant L15A Forming Cr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gq5
TitleCrystal Structure of the PSMalpha3 Peptide Mutant L15A Forming Cross-Alpha Amyloid-like Fibril
ComponentsPhenol-soluble modulin alpha 3 peptide
KeywordsPROTEIN FIBRIL / cross-alpha / fibril / amyloid / mating alpha-helical sheets
Function / homology: / Phenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / killing of cells of another organism / Phenol-soluble modulin alpha 3 peptide
Function and homology information
Biological speciesStaphylococcus aureus RF122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
Model detailsS. aureus
AuthorsLandau, M. / Tayeb-Fligelman, E.
CitationJournal: Structure / Year: 2020
Title: Staphylococcus aureus PSM alpha 3 Cross-alpha Fibril Polymorphism and Determinants of Cytotoxicity.
Authors: Tayeb-Fligelman, E. / Salinas, N. / Tabachnikov, O. / Landau, M.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.3Jan 17, 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: Phenol-soluble modulin alpha 3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6872
Polymers2,5691
Non-polymers1181
Water19811
1
A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,37036
Polymers46,24318
Non-polymers2,12718
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation1_595x,y+4,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_525x,y-3,z1
crystal symmetry operation1_515x,y-4,z1
crystal symmetry operation2_414-x-1,y-7/2,-z-11
crystal symmetry operation2_424-x-1,y-5/2,-z-11
crystal symmetry operation2_434-x-1,y-3/2,-z-11
crystal symmetry operation2_444-x-1,y-1/2,-z-11
crystal symmetry operation2_454-x-1,y+1/2,-z-11
crystal symmetry operation2_464-x-1,y+3/2,-z-11
crystal symmetry operation2_474-x-1,y+5/2,-z-11
crystal symmetry operation2_484-x-1,y+7/2,-z-11
crystal symmetry operation2_494-x-1,y+9/2,-z-11
Unit cell
Length a, b, c (Å)28.410, 10.670, 29.600
Angle α, β, γ (deg.)90.000, 105.870, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide Phenol-soluble modulin alpha 3 peptide


Mass: 2569.069 Da / Num. of mol.: 1 / Fragment: PSMalpha3 full-length mutant (residues 1-22) / Mutation: L15A / Source method: obtained synthetically / Details: PSMalpha3 L15A mutant, synthesized / Source: (synth.) Staphylococcus aureus RF122 / References: UniProt: P0C807
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 26.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.1 M CAPS pH 10.5, 40% v/v 2-Methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→17.47 Å / Num. obs: 2854 / % possible obs: 96.3 % / Redundancy: 2.68 % / Biso Wilson estimate: 20.678 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.137 / Rrim(I) all: 0.171 / Χ2: 0.957 / Net I/σ(I): 4.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.542.6520.5591.562070.8510.69295
1.54-1.582.5850.4761.682050.8410.60399
1.58-1.632.7510.4921.821810.8530.61197.8
1.63-1.682.7250.4672.082040.6820.59897.1
1.68-1.732.7580.3722.751900.7750.463100
1.73-1.792.7490.3512.641990.8860.43896.6
1.79-1.862.5950.3322.831580.8150.42499.4
1.86-1.942.7080.2543.421610.8960.31897
1.94-2.022.820.2184.111670.9150.26896
2.02-2.122.7090.1835.121580.9310.22597.5
2.12-2.242.5880.1585.251480.9370.19794.9
2.24-2.372.5230.1646.021320.9290.20692.3
2.37-2.542.3140.2015.541180.8980.24586.8
2.54-2.742.8530.1446.51290.9460.17697
2.74-32.7330.1246.661050.9750.15398.1
3-3.362.8770.1287.511140.9480.15896.6
3.36-3.872.5910.0877.38930.9920.10897.9
3.87-4.752.7230.0877.84830.980.1194.3
4.75-6.712.7540.0797.85610.9910.09793.8
6.71-17.472.2930.0446.99410.9980.05587.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I55

5i55


Resolution: 1.5→17.47 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.272 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.108
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 286 10 %RANDOM
Rwork0.1943 ---
obs0.1995 2568 96.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 46.49 Å2 / Biso mean: 18.714 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20.94 Å2
2---0.3 Å20 Å2
3----1.93 Å2
Refinement stepCycle: final / Resolution: 1.5→17.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms182 0 8 11 201
Biso mean--41.26 23.33 -
Num. residues----22
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02193
X-RAY DIFFRACTIONr_bond_other_d0.0490.02197
X-RAY DIFFRACTIONr_angle_refined_deg1.6922.005255
X-RAY DIFFRACTIONr_angle_other_deg2.6713452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.581521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.48824.4449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0941536
X-RAY DIFFRACTIONr_chiral_restr0.0960.226
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02202
X-RAY DIFFRACTIONr_gen_planes_other0.0230.0246
LS refinement shellResolution: 1.5→1.676 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.361 79 -
Rwork0.334 713 -
all-792 -
obs--97.42 %

+
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