[English] 日本語
Yorodumi
- PDB-4oov: Crystal structure of P domain from norovirus strain Farmington Hi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oov
TitleCrystal structure of P domain from norovirus strain Farmington Hills 2004
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / VIRAL CAPSID PROTEIN / Protruding Domain
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Major capsid protein
Similarity search - Component
Biological speciesNorovirus Hu/GII.4/Farmington Hills/2004/USA
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsSingh, B.K. / Leuthold, M. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Human noroviruses' fondness for histo-blood group antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.
History
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Major capsid protein
B: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,07010
Polymers67,5732
Non-polymers4978
Water13,962775
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint7 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.950, 90.120, 109.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 224 - 530 / Label seq-ID: 1 - 307

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Major capsid protein


Mass: 33786.648 Da / Num. of mol.: 2 / Fragment: unp residues 225-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Farmington Hills/2004/USA
Gene: JQ478408 / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R4I4P2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97939 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.5→99.219 Å / Num. obs: 99095 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 12.14 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.941 / Net I/σ(I): 14.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.540.562.2727638707797
1.54-1.580.4713.1835308708399.6
1.58-1.630.4083.7834875688199.4
1.63-1.680.3384.5233451669699.7
1.68-1.730.2875.1531371649399.4
1.73-1.790.2266.3830517629099.4
1.79-1.860.1858.0331341607699.3
1.86-1.940.1649.2529680585599.3
1.94-2.020.12711.3827786559699.5
2.02-2.120.10213.2924869536599.1
2.12-2.240.08816.0926547512699.6
2.24-2.370.07718.524869487899.5
2.37-2.540.06620.4823272458599.6
2.54-2.740.05722.2119993427299.2
2.74-30.04827.7120736395699.5
3-3.360.03735.1418431358399.5
3.36-3.880.03239.5815127318599.3
3.88-4.750.02846.813375270599
4.75-6.710.0343.8910516214399.4
6.710.02846.225595125097.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→99.219 Å / FOM work R set: 0.9112 / SU ML: 0.11 / σ(F): 1.36 / Phase error: 15.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1709 4684 5 %
Rwork0.1448 --
obs0.1461 93719 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.84 Å2 / Biso mean: 15.8 Å2 / Biso min: 5.21 Å2
Refinement stepCycle: LAST / Resolution: 1.53→99.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 32 775 5543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094925
X-RAY DIFFRACTIONf_angle_d1.296731
X-RAY DIFFRACTIONf_chiral_restr0.055738
X-RAY DIFFRACTIONf_plane_restr0.007898
X-RAY DIFFRACTIONf_dihedral_angle_d12.2661753
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2810X-RAY DIFFRACTION5.229TORSIONAL
12B2810X-RAY DIFFRACTION5.229TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.53-1.54740.25721530.20592915306899
1.5474-1.56560.21691560.193929543110100
1.5656-1.58470.23381530.185629333086100
1.5847-1.60470.22221550.18492937309299
1.6047-1.62590.20671530.17782914306799
1.6259-1.64810.19891550.174729633118100
1.6481-1.67170.1991540.163929223076100
1.6717-1.69660.19751550.159729503105100
1.6966-1.72320.19311540.16312929308399
1.7232-1.75140.21071550.16242949310499
1.7514-1.78160.20041540.15662927308199
1.7816-1.8140.19381550.15392943309899
1.814-1.84890.20461570.1462979313699
1.8489-1.88660.17121540.15042940309499
1.8866-1.92770.18631540.1452918307299
1.9277-1.97250.16271560.14042961311799
1.9725-2.02180.16871540.131829483102100
2.0218-2.07650.16541550.13182945310099
2.0765-2.13760.1481550.13032945310099
2.1376-2.20660.14871580.129829943152100
2.2066-2.28550.14151560.12312963311999
2.2855-2.3770.15011560.128429573113100
2.377-2.48510.17331570.130929853142100
2.4851-2.61610.16361580.137330123170100
2.6161-2.780.15851560.14042957311399
2.78-2.99460.14891580.14530103168100
2.9946-3.29590.17561590.14233018317799
3.2959-3.77270.17711590.14393031319099
3.7727-4.75250.12871600.12943043320399
4.7525-46.72290.17851700.16023193336399

+
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