[English] 日本語
Yorodumi
- PDB-6fgr: Crystal Structure of the Amyloid-like IIKIIK Segment from the S. ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fgr
TitleCrystal Structure of the Amyloid-like IIKIIK Segment from the S. aureus Biofilm-associated PSMalpha4
ComponentsPsm alpha-4
KeywordsPROTEIN FIBRIL / steric-zipper / cross-beta / bacterial amyloid fibril / S. aureus / PSM
Function / homologyPhenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / : / Phenol-soluble modulin alpha 4 peptide
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
Model detailsPhenol Soluble Modulin
AuthorsLandau, M. / Colletier, J.-P.
Funding support Israel, 4items
OrganizationGrant numberCountry
Israel Science Foundation560/16 Israel
Deutsch-IsraelischeProjektkooperation (DIP)3655/1-1 Israel
I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation1775/12 Israel
United States - Israel Binational Science Foundation (BSF)2013254 Israel
CitationJournal: Nat Commun / Year: 2018
Title: Extreme amyloid polymorphism in Staphylococcus aureus virulent PSM alpha peptides.
Authors: Salinas, N. / Colletier, J.P. / Moshe, A. / Landau, M.
History
DepositionJan 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Psm alpha-4
A: Psm alpha-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7125
Polymers1,4582
Non-polymers2543
Water543
1
B: Psm alpha-4
A: Psm alpha-4
hetero molecules

B: Psm alpha-4
A: Psm alpha-4
hetero molecules

B: Psm alpha-4
A: Psm alpha-4
hetero molecules

B: Psm alpha-4
A: Psm alpha-4
hetero molecules

B: Psm alpha-4
A: Psm alpha-4
hetero molecules

B: Psm alpha-4
A: Psm alpha-4
hetero molecules

B: Psm alpha-4
A: Psm alpha-4
hetero molecules

B: Psm alpha-4
A: Psm alpha-4
hetero molecules

B: Psm alpha-4
A: Psm alpha-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,41045
Polymers13,12218
Non-polymers2,28827
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_155x-4,y,z1
crystal symmetry operation1_255x-3,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_855x+3,y,z1
crystal symmetry operation1_955x+4,y,z1
Unit cell
Length a, b, c (Å)4.830, 22.380, 23.060
Angle α, β, γ (deg.)107.000, 90.010, 96.200
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein/peptide Psm alpha-4


Mass: 729.006 Da / Num. of mol.: 2
Fragment: Amyloid spine segment IIKIIK from PSMalpha4 (residues 7-12) secreted by S. aureus
Source method: obtained synthetically / Details: IIKIIK from PSMalpha4, synthesized / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: H9BRQ8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1.62 Å3/Da / Density % sol: 24.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.2M Ammonium sulfate, 20% polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.5→18.21 Å / Num. obs: 1397 / % possible obs: 95 % / Redundancy: 9.89 % / Biso Wilson estimate: 16.205 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.206 / Rrim(I) all: 0.217 / Χ2: 0.835 / Net I/σ(I): 7.18 / Num. measured all: 13816 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.564.8730.6222.397701771580.7440.69489.3
1.56-1.626.5690.4473.447161471090.920.48474.1
1.62-1.699.5940.5473.7212761341330.8570.57799.3
1.69-1.7810.4580.5214.2612341181180.8790.55100
1.78-1.8710.7420.384.812891211200.9710.39999.2
1.87-1.9911.4240.2517.9714281261250.990.26299.2
1.99-2.1211.7460.268.2915271311300.9770.27299.2
2.12-2.29120.2239.9714641181220.9840.233100
2.29-2.519.5170.2148.64847101890.9920.22688.1
2.51-2.8110.5070.1799.776775730.9960.18897.3
2.81-3.2410.6520.18210.1473569690.9960.19100
3.24-3.9711.3780.1514.284274740.9940.156100
3.97-5.6211.930.12616.5168058570.9890.13298.3
5.62-18.2112.050.09612.38241222010.190.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO / Packing: 0

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal beta-strand of poly-ala

Resolution: 1.5→18.21 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2222 / WRfactor Rwork: 0.1868 / FOM work R set: 0.8212 / SU B: 4.347 / SU ML: 0.071 / SU R Cruickshank DPI: 0.3052 / SU Rfree: 0.1113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 140 10 %RANDOM
Rwork0.1828 ---
obs0.1869 1257 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.86 Å2 / Biso mean: 9.128 Å2 / Biso min: 1.71 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0.05 Å20 Å2
2---0.3 Å2-0.13 Å2
3---0.33 Å2
Refinement stepCycle: final / Resolution: 1.5→18.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms102 0 22 3 127
Biso mean--30.37 26.93 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02117
X-RAY DIFFRACTIONr_bond_other_d0.0190.02159
X-RAY DIFFRACTIONr_angle_refined_deg1.9032.226148
X-RAY DIFFRACTIONr_angle_other_deg0.9583365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.356510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7691532
X-RAY DIFFRACTIONr_chiral_restr0.120.222
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210
X-RAY DIFFRACTIONr_rigid_bond_restr8.1463276
X-RAY DIFFRACTIONr_sphericity_free8.67651
X-RAY DIFFRACTIONr_sphericity_bonded2.7095285
LS refinement shellResolution: 1.502→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 11 -
Rwork0.264 96 -
all-107 -
obs--93.86 %

+
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://pdbjlvh1.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