[English] 日本語
Yorodumi
- PDB-5nbh: Structure of the distal domain of mouse adenovirus 2 fibre, P2121... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nbh
TitleStructure of the distal domain of mouse adenovirus 2 fibre, P212121 native
ComponentsFiber
KeywordsVIRAL PROTEIN / Triple beta-spiral / 3-bladed propeller / ABCJ-GHID topology / N-acetyl-glucosamine binding
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / virion component / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily
Similarity search - Domain/homology
Biological speciesMurine adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSingh, A.K. / van Raaij, M.J.
CitationJournal: J. Gen. Virol. / Year: 2018
Title: Structure and N-acetylglucosamine binding of the distal domain of mouse adenovirus 2 fibre.
Authors: Singh, A.K. / Nguyen, T.H. / Vidovszky, M.Z. / Harrach, B. / Benko, M. / Kirwan, A. / Joshi, L. / Kilcoyne, M. / Berbis, M.A. / Canada, F.J. / Jimenez-Barbero, J. / Menendez, M. / Wilson, S. ...Authors: Singh, A.K. / Nguyen, T.H. / Vidovszky, M.Z. / Harrach, B. / Benko, M. / Kirwan, A. / Joshi, L. / Kilcoyne, M. / Berbis, M.A. / Canada, F.J. / Jimenez-Barbero, J. / Menendez, M. / Wilson, S.S. / Bromme, B.A. / Smith, J.G. / van Raaij, M.J.
History
DepositionMar 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _entity.formula_weight
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
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: Fiber
B: Fiber
C: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5254
Polymers77,4333
Non-polymers921
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Protein is trimeric on SDS-PAGE gels if sample is not boiled prior to electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-81 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.872, 91.110, 128.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Fiber


Mass: 25810.922 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine adenovirus 2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E7CH51
#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.: 672 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mM Tris-HCl, 10 % (w/v) PEG 4000, 0.1 M HEPES-NaOH, 0.1 M magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→34.1 Å / Num. obs: 68912 / % possible obs: 94.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.5 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.3
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3722 / CC1/2: 0.857 / % possible all: 69.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N8D

5n8d


Resolution: 1.7→34.05 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.497 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.109 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21621 3559 5.2 %THIN SHELLS
Rwork0.17182 ---
obs0.17422 65280 94.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2--0.37 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.7→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4515 0 6 672 5193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024730
X-RAY DIFFRACTIONr_bond_other_d0.0020.024215
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9556445
X-RAY DIFFRACTIONr_angle_other_deg0.88939821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6385605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25123.913207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51315769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5451524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021012
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_it1.6751.8222351
X-RAY DIFFRACTIONr_mcbond_other1.6731.8212350
X-RAY DIFFRACTIONr_mcangle_it2.8072.7172940
X-RAY DIFFRACTIONr_mcangle_other2.8082.7182941
X-RAY DIFFRACTIONr_scbond_it2.112.0662379
X-RAY DIFFRACTIONr_scbond_other2.1092.0662379
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3223.0163493
X-RAY DIFFRACTIONr_long_range_B_refined6.0923.2975273
X-RAY DIFFRACTIONr_long_range_B_other5.80422.5145085
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.817 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.266 540 -
Rwork0.257 9409 -
obs--76.19 %

+
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