[English] 日本語
Yorodumi
- PDB-3riq: Siphovirus 9NA tailspike receptor binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3riq
TitleSiphovirus 9NA tailspike receptor binding domain
ComponentsTailspike protein
KeywordsVIRAL PROTEIN / right handed beta-helix / tailspike / endorhamnosidase / lipopolysaccharide
Function / homology
Function and homology information


biological process involved in interaction with host / viral life cycle / virion component
Similarity search - Function
Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Pectate Lyase C-like - #20 / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Autotransporter, pectate lyase C-like domain superfamily / Pectate Lyase C-like / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesSiphovirus 9NA
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAndres, D. / Roske, Y. / Doering, C. / Heinemann, U. / Seckler, R. / Barbirz, S.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: Tail morphology controls DNA release in two Salmonella phages with one lipopolysaccharide receptor recognition system.
Authors: Andres, D. / Roske, Y. / Doering, C. / Heinemann, U. / Seckler, R. / Barbirz, S.
History
DepositionApr 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4982
Polymers59,4061
Non-polymers921
Water12,629701
1
A: Tailspike protein
hetero molecules

A: Tailspike protein
hetero molecules

A: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,4956
Polymers178,2193
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area27910 Å2
ΔGint-127 kcal/mol
Surface area49850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.132, 149.132, 149.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-765-

HOH

21A-767-

HOH

31A-773-

HOH

41A-818-

HOH

51A-833-

HOH

61A-957-

HOH

71A-964-

HOH

81A-1127-

HOH

-
Components

#1: Protein Tailspike protein


Mass: 59406.215 Da / Num. of mol.: 1
Fragment: C-terminal fragment, receptor binding domain, residues 131-673
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siphovirus 9NA / Plasmid: pET 11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8GV21*PLUS
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 20% PEG 5000 MME, 0.1M BisTris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 23, 2010
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.5→33.3 Å / Num. obs: 87485 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.065 / Net I/σ(I): 15.6
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 2.59 / Rsym value: 0.686 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VFM

2vfm


Resolution: 1.5→33.35 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.332 / SU ML: 0.039 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1695 4372 5 %RANDOM
Rwork0.12773 ---
obs0.12984 83067 100 %-
all-87485 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.858 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 6 701 4861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224317
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9375884
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6185563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18424.874199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50515700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4041520
X-RAY DIFFRACTIONr_chiral_restr0.1070.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213322
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4021.52712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.15424388
X-RAY DIFFRACTIONr_scbond_it3.38631605
X-RAY DIFFRACTIONr_scangle_it4.8184.51486
X-RAY DIFFRACTIONr_rigid_bond_restr1.61134317
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 320 -
Rwork0.157 6089 -
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