[English] 日本語
Yorodumi
- PDB-4rdj: Crystal structure of Norovirus Boxer P domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rdj
TitleCrystal structure of Norovirus Boxer P domain
ComponentsCapsid
KeywordsVIRAL PROTEIN / mixed alpha/beta structure / virus capsid / receptor binding / HBGA
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / 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 / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman calicivirus NLV/Boxer/2001/US
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHao, N. / Chen, Y. / Xia, M. / Liu, W. / Tan, M. / Jiang, X. / Li, X.
CitationJournal: Protein Cell / Year: 2015
Title: Crystal structures of GI.8 Boxer virus P dimers in complex with HBGAs, a novel evolutionary path selected by the Lewis epitope.
Authors: Hao, N. / Chen, Y. / Xia, M. / Tan, M. / Liu, W. / Guan, X. / Jiang, X. / Li, X. / Rao, Z.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid
B: Capsid


Theoretical massNumber of molelcules
Total (without water)67,5182
Polymers67,5182
Non-polymers00
Water13,763764
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-28 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.867, 139.867, 64.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Capsid /


Mass: 33758.879 Da / Num. of mol.: 2 / Fragment: Protrusion domain, UNP residues 227-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human calicivirus NLV/Boxer/2001/US / Plasmid: pGex-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8BCA3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M LiCl, 18% (w/v) PEG 3350, 10% (v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 115571 / Num. obs: 115571 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 42.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 11 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 5.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZL7

2zl7


Resolution: 1.5→29.377 Å / SU ML: 0.15 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1627 5825 5.05 %RANDOM
Rwork0.1362 ---
obs0.1375 115416 99.99 %-
all-115416 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.44 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.3383 Å2-0 Å2-0 Å2
2--1.3383 Å2-0 Å2
3----2.6767 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 0 764 5316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064714
X-RAY DIFFRACTIONf_angle_d1.0576458
X-RAY DIFFRACTIONf_dihedral_angle_d12.321708
X-RAY DIFFRACTIONf_chiral_restr0.074710
X-RAY DIFFRACTIONf_plane_restr0.005864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.5-1.5170.21471960.14653637
1.517-1.53490.20542150.13743607
1.5349-1.55360.19611980.13763672
1.5536-1.57330.19711840.13743631
1.5733-1.5940.17912010.13413625
1.594-1.61580.1721950.13283629
1.6158-1.63890.17561950.12453656
1.6389-1.66340.1821930.12723589
1.6634-1.68930.15032110.12023620
1.6893-1.7170.16262000.11643668
1.717-1.74660.16841890.11623620
1.7466-1.77840.15551680.11163655
1.7784-1.81260.17291880.11163657
1.8126-1.84960.15931900.1173655
1.8496-1.88980.14692040.11563628
1.8898-1.93370.15622000.11853613
1.9337-1.98210.15591880.11713674
1.9821-2.03570.15471960.12243605
2.0357-2.09560.13261870.12193680
2.0956-2.16320.15422020.12733671
2.1632-2.24050.17491990.12853625
2.2405-2.33010.14421980.12533659
2.3301-2.43610.14781770.12683652
2.4361-2.56450.15221860.13853684
2.5645-2.72510.18281990.14893660
2.7251-2.93530.16841830.14393669
2.9353-3.23040.17541810.14583720
3.2304-3.6970.16891980.14483658
3.697-4.65490.1281950.13243712
4.6549-29.38250.18672090.17963760

+
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