5GVU

crystal structure of BVDV NS3 helicase domain

> Summary

Summary for 5GVU

DescriptorNS3 helicase (2 entities in total)
Functional Keywordshelicase, ns3, bvdv, flavivirus, pestivirus, hydrolase
Biological sourceBovine viral diarrhea virus 1 (BVDV)
Total number of polymer chains3
Total molecular weight159863.42
Authors
Li, S.,Mao, X. (deposition date: 2016-09-06, release date: 2017-09-13)
Primary citation
Shi, J.,He, M.,Nie, Y.,Li, S.,Mao, X.
crystal structure of BVDV NS3 helicase
To Be Published,
Experimental method
X-RAY DIFFRACTION (2.82 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.29950.3%8.1%10.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5gvu
no rotation
Molmil generated image of 5gvu
rotated about x axis by 90°
Molmil generated image of 5gvu
rotated about y axis by 90°

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight159863.4
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight159863.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.82 Å)

Cell axes121.100121.100109.721
Cell angles90.0090.00120.00
SpacegroupP 32
Resolution limits50.01 - 2.82
the highest resolution shell value2.893 - 2.820
R-factor0.2732
R-work0.27190
the highest resolution shell value0.307
R-free0.29840
the highest resolution shell value0.357
RMSD bond length0.008
RMSD bond angle1.361

Data Collection Statistics

Resolution limits50.01 - 2.82
the highest resolution shell value -
Number of reflections41208
the highest resolution shell value0.451
Completeness100.0
Redundancy15
the highest resolution shell value15.3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP293

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

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5gvu.ent.gz (393.33 KB)
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all (no-compress)pdb5gvu.ent (1.52 MB)
header onlypdb5gvu.ent.gz (9.09 KB)
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PDBx/mmCIF5gvu.cif.gz (461.3 KB)
PDBMLall5gvu.xml.gz (632.55 KB)
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no-atom5gvu-noatom.xml.gz (40.26 KB)
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ext-atom5gvu-extatom.xml.gz (212.48 KB)
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PDBMLplusall5gvu-plus.xml.gz (633.27 KB)
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no-atom5gvu-plus-noatom.xml.gz (40.99 KB)
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add only5gvu-add.xml.gz (743 B)
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RDF5gvu.rdf.gz (96.78 KB)
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Structure factorsr5gvusf.ent.gz (905.24 KB)
Biological unit (PDB format)5gvu.pdb1.gz (150.62 KB) (A)
*author defined assembly, 1 molecule(s) (monomeric)
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5gvu.pdb2.gz (118.53 KB) (B)
*author defined assembly, 1 molecule(s) (monomeric)
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5gvu.pdb3.gz (126.37 KB) (C)
*author defined assembly, 1 molecule(s) (monomeric)
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Validation reportsPDF5gvu​_validation.pdf.gz (276.29 KB)
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PDF-full5gvu​_full​_validation.pdf.gz (299.12 KB)
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XML5gvu​_validation.xml.gz (39.36 KB)
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PNG5gvu​_multipercentile​_validation.png.gz (161.64 KB)
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SVG5gvu​_multipercentile​_validation.svg.gz (947 B)
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Sequence (fasta)5gvu​_seq.txt
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