3R6J

Crystal Structure of the Capsid P Domain from Norwalk Virus Strain Hiroshima/1999

> Summary

Summary for 3R6J

Related3R6K 3PA1 3PA2 3Q38 3Q39 3Q3A 3Q6Q 3Q6R 3ONY 3ONU
DescriptorVP1 protein
Functional Keywordsnorovirus, p-domain, capsid, receptor, histo blood group antigen (hbga), viral protein
Biological sourceNorwalk-like virus
Total number of polymer chains1
Total molecular weight33476.87
Authors
Hansman, G.S.,Biertumpfel, C.,McLellan, J.S.,Georgiev, I.,Chen, L.,Zhou, T.,Katayama, K.,Kwong, P.D. (deposition date: 2011-03-21, release date: 2011-05-11, modification date: 2011-11-02)
Primary citation
Hansman, G.S.,Biertumpfel, C.,Georgiev, I.,McLellan, J.S.,Chen, L.,Zhou, T.,Katayama, K.,Kwong, P.D.
Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability.
J.Virol., 85:6687-6701, 2011
PubMed: 21525337
DOI: 10.1128/JVI.00246-11
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.75 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.199700.8%15.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 3r6j
no rotation
Molmil generated image of 3r6j
rotated about x axis by 90°
Molmil generated image of 3r6j
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 3r6j
no rotation
Molmil generated image of 3r6j
rotated about x axis by 90°
Molmil generated image of 3r6j
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (3r6j.pdb1.gz [203.2 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AVP1 proteinpolymer30533414.81
UniProt (Q54AD6)
Pfam (PF00915)
Pfam (PF08435)
Norwalk-like virus
1,2-ETHANEDIOLnon-polymer62.11
waterwater18.0124

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight33414.8
Non-Polymers*Number of molecules1
Total molecular weight62.1
All*Total molecular weight33476.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.75 Å)

Cell axes73.15499.12177.590
Cell angles90.0090.0090.00
SpacegroupC 2 2 21
Resolution limits24.78 - 1.75
the highest resolution shell value1.813 - 1.750
R-factor0.1867
R-work0.18580
the highest resolution shell value0.260
R-free0.20380
the highest resolution shell value0.303
RMSD bond length0.004
RMSD bond angle0.837

Data Collection Statistics

Resolution limits24.78 - 1.75
the highest resolution shell value -
Number of reflections28503
Completeness98.9
Redundancy5.1
the highest resolution shell value3.9
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.5293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16BINDING SITE FOR RESIDUE EDO A 1
ChainResidue
AHOH9
AHOH24
AHOH24
ALEU232
AGLU451
AHIS455

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
EDO_3r6j_A_151,2-ETHANEDIOL binding site
ChainResidueligand
APRO230EDO: 1,2-ETHANEDIOL
ALEU232EDO: 1,2-ETHANEDIOL
AGLU451EDO: 1,2-ETHANEDIOL
AGLN454-HIS455EDO: 1,2-ETHANEDIOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS004301TonB-dependent receptor proteins signature 1.
ChainResidueDetails
ANA*

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Fucose.
ChainResidueDetails
AASP155

SWS_FT_FI21Fucose; via amide nitrogen.
ChainResidueDetails
AGLY218

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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