5GVI

Zebrafish USP30 in complex with Lys6-linked diubiquitin

> Summary

Summary for 5GVI

DescriptorUbiquitin carboxyl-terminal hydrolase 30, ubiquitin, ZINC ION, ... (5 entities in total)
Functional Keywordscomplex, mitophagy, hydrolase-signaling protein complex, hydrolase/signaling protein
Biological sourceDanio rerio (Zebrafish)
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Cellular locationUbiquitin: Cytoplasm  P62983 P62983
Total number of polymer chains3
Total molecular weight67355.39
Authors
Sato, Y.,Fukai, S. (deposition date: 2016-09-05, release date: 2017-09-13)
Primary citation
Sato, Y.,Okatsu, K.,Yamagata, A.,Goto-Ito, S.,Ishikawa, M.,Hashimoto, Y.,Fukai, S.
Structural basis for specific recognition of Lys6-linked polyubiquitin chains by USP30
To Be Published,
Experimental method
X-RAY DIFFRACTION (1.87 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.207300.9%10.5%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight67290.0
Non-Polymers*Number of molecules1
Total molecular weight65.4
All*Total molecular weight67355.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.87 Å)

Cell axes130.270130.27059.881
Cell angles90.0090.00120.00
SpacegroupP 65
Resolution limits44.08 - 1.87
the highest resolution shell value1.908 - 1.870
R-factor0.1779
R-work0.17640
the highest resolution shell value0.275
R-free0.20600
the highest resolution shell value0.303
RMSD bond length0.006
RMSD bond angle1.022

Data Collection Statistics

Resolution limits50.00 - 1.87
the highest resolution shell value -
Number of reflections47938
Completeness99.6
Redundancy7.9
the highest resolution shell value5.1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP9293

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
AC14binding site for residue ZN A 601
ChainResidue
ACYS230
ACYS233
ACYS280
ACYS283

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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
SWS_FT_FI12Activating enzyme.
ChainResidueDetails
BARG54
BARG72

SWS_FT_FI21Essential for function.
ChainResidueDetails
BHIS68

SWS_FT_FI32Activating enzyme.
ChainResidueDetails
CARG54
CARG72

SWS_FT_FI41Essential for function.
ChainResidueDetails
CHIS68

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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