[English] 日本語
Yorodumi
- PDB-6g8c: Crystal Structure of the Amyloid-like IYQYGG segment from the R1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g8c
TitleCrystal Structure of the Amyloid-like IYQYGG segment from the R1 repeat of the E. coli Biofilm-associated CsgA Curli protein
ComponentsMajor curlin subunit
KeywordsPROTEIN FIBRIL / Bacterial steric-zipper cross-beta amyloid fibril from E. coli
Function / homologyCurlin associated / Curlin associated repeat / regulation of amyloid fibril formation / single-species biofilm formation / pilus / amyloid fibril formation / cell adhesion / identical protein binding / Major curlin subunit
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
Model detailsCurli
AuthorsLandau, M. / Perov, S.
CitationJournal: Plos Pathog. / Year: 2019
Title: Structural Insights into Curli CsgA Cross-beta Fibril Architecture Inspire Repurposing of Anti-amyloid Compounds as Anti-biofilm Agents.
Authors: Perov, S. / Lidor, O. / Salinas, N. / Golan, N. / Tayeb-Fligelman, E. / Deshmukh, M. / Willbold, D. / Landau, M.
History
DepositionApr 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 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
B: Major curlin subunit


Theoretical massNumber of molelcules
Total (without water)7001
Polymers7001
Non-polymers00
Water362
1
B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit

B: Major curlin subunit


Theoretical massNumber of molelcules
Total (without water)12,59618
Polymers12,59618
Non-polymers00
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,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 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 operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation4_515-x+1/2,y-7/2,-z1
crystal symmetry operation4_525-x+1/2,y-5/2,-z1
crystal symmetry operation4_535-x+1/2,y-3/2,-z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
crystal symmetry operation4_565-x+1/2,y+3/2,-z1
crystal symmetry operation4_575-x+1/2,y+5/2,-z1
crystal symmetry operation4_585-x+1/2,y+7/2,-z1
crystal symmetry operation4_595-x+1/2,y+9/2,-z1
Unit cell
Length a, b, c (Å)42.170, 4.760, 19.600
Angle α, β, γ (deg.)90.000, 102.430, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein/peptide Major curlin subunit


Mass: 699.753 Da / Num. of mol.: 1
Fragment: Amyloid spine segment IYQYGG from CsgA (residues 47-52) secreted by E. coli
Source method: obtained synthetically / Details: IYQYGG from CsgA, synthesized / Source: (synth.) Escherichia coli K-12 (bacteria) / References: UniProt: P28307
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDescription: needle-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.1 M Sodium acetate pH 4.6 and 2.0 M Sodium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→19.14 Å / Num. obs: 545 / % possible obs: 97.3 % / Redundancy: 5.231 % / Biso Wilson estimate: 19.055 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.111 / Χ2: 1.116 / Net I/σ(I): 8.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.855.9010.3263.211410.9770.359100
1.85-2.135.4540.1886.931410.9760.2198.6
2.13-2.614.890.129.581090.9910.13694
2.61-3.694.9160.06613.42950.9970.07499
3.69-19.144.2370.05416.47590.9960.06290.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.65 Å19.14 Å
Translation1.65 Å19.14 Å

-
Processing

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

Resolution: 1.65→19.14 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.799 / SU ML: 0.056 / SU R Cruickshank DPI: 0.1077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.1
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1779 55 10.1 %RANDOM
Rwork0.1449 ---
obs0.1478 489 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 26.07 Å2 / Biso mean: 11.969 Å2 / Biso min: 8.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20.28 Å2
2---0.81 Å20 Å2
3---1.69 Å2
Refinement stepCycle: final / Resolution: 1.65→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50 0 0 2 52
Biso mean---25.53 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0251
X-RAY DIFFRACTIONr_bond_other_d0.0020.0241
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.98168
X-RAY DIFFRACTIONr_angle_other_deg0.918394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.76323.3333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.945156
X-RAY DIFFRACTIONr_chiral_restr0.110.25
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0259
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0213
LS refinement shellResolution: 1.652→1.694 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 4 -
Rwork0.32 32 -
all-36 -
obs--100 %

+
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