[English] 日本語
Yorodumi
- PDB-8uus: Structure of Serratia proteamaculans antifeeding prophage Fibre f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uus
TitleStructure of Serratia proteamaculans antifeeding prophage Fibre foot domain (AfpX13)
ComponentsAntifeeding Prophage (Tailocin) fibre
KeywordsSTRUCTURAL PROTEIN / Anti-feeding prophage / Fibre foot / Cell binding
Function / homologyAttachment protein shaft domain superfamily / Parallel beta-helix repeat / Parallel beta-helix repeats / virion attachment to host cell / CITRIC ACID / AMMONIUM ION / AfpX13
Function and homology information
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsYoung, P.G. / Hurst, M.R.H.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Ministry of Business, Innovation and Employment (New Zealand)C10X1805 New Zealand
CitationJournal: To Be Published
Title: Structure of Serratia entomophila antifeeding prophage Fibre foot domain (Afp13)
Authors: Young, P.G. / Hurst, M.R.H.
History
DepositionNov 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antifeeding Prophage (Tailocin) fibre
B: Antifeeding Prophage (Tailocin) fibre
C: Antifeeding Prophage (Tailocin) fibre
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6448
Polymers51,1573
Non-polymers4865
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-93 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.113, 68.241, 111.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein Antifeeding Prophage (Tailocin) fibre / AfpX13


Mass: 17052.398 Da / Num. of mol.: 3 / Fragment: foot domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (bacteria) / Strain: AGR96X / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): Shuffle T7 / References: UniProt: A0A2R2Q2I2
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.94 % / Description: Rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 3350, 0.15 M Ammonium citrate / PH range: 4.5 - 4.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953725 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 1.47→44.6 Å / Num. obs: 77498 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 16.91 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.061 / Net I/σ(I): 10
Reflection shellResolution: 1.47→1.49 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3684 / CC1/2: 0.521 / Rpim(I) all: 1.112 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→32.62 Å / SU ML: 0.1673 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.4094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 3886 5.02 %
Rwork0.1931 73493 -
obs0.1946 77379 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.31 Å2
Refinement stepCycle: LAST / Resolution: 1.47→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 32 274 3765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573542
X-RAY DIFFRACTIONf_angle_d0.9124801
X-RAY DIFFRACTIONf_chiral_restr0.0924571
X-RAY DIFFRACTIONf_plane_restr0.0046597
X-RAY DIFFRACTIONf_dihedral_angle_d9.8595519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.3471520.32442485X-RAY DIFFRACTION96.17
1.49-1.510.31251520.28912594X-RAY DIFFRACTION99.89
1.51-1.530.2931280.27732570X-RAY DIFFRACTION99.82
1.53-1.550.25461390.25512595X-RAY DIFFRACTION99.93
1.55-1.570.26961370.23912590X-RAY DIFFRACTION99.93
1.57-1.590.27281350.24332641X-RAY DIFFRACTION100
1.59-1.620.28781300.24192583X-RAY DIFFRACTION99.93
1.62-1.640.29371430.23262608X-RAY DIFFRACTION100
1.64-1.670.25671540.22332575X-RAY DIFFRACTION99.96
1.67-1.70.27681400.22822590X-RAY DIFFRACTION99.93
1.7-1.730.24981140.22152622X-RAY DIFFRACTION100
1.73-1.770.26521230.22052621X-RAY DIFFRACTION100
1.77-1.810.2651270.22342619X-RAY DIFFRACTION100
1.81-1.850.24941330.20272633X-RAY DIFFRACTION100
1.85-1.90.20011290.18552601X-RAY DIFFRACTION100
1.9-1.950.22481050.18672646X-RAY DIFFRACTION100
1.95-2.010.22761630.1832605X-RAY DIFFRACTION100
2.01-2.070.19361490.17592595X-RAY DIFFRACTION100
2.07-2.140.22431280.18622638X-RAY DIFFRACTION100
2.14-2.230.22431540.17952603X-RAY DIFFRACTION99.96
2.23-2.330.25081090.18592670X-RAY DIFFRACTION100
2.33-2.450.22691460.19642636X-RAY DIFFRACTION100
2.45-2.610.21251380.19672641X-RAY DIFFRACTION100
2.61-2.810.22581520.19672662X-RAY DIFFRACTION100
2.81-3.090.20231470.19322643X-RAY DIFFRACTION100
3.09-3.540.19391580.17512671X-RAY DIFFRACTION100
3.54-4.460.20451490.16092708X-RAY DIFFRACTION100
4.46-100.21271520.18292848X-RAY DIFFRACTION99.93

+
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