5B62

Crystal structure of N-terminal amidase with Asn-Glu-Ala peptide

> Summary

Summary for 5B62

Related5K5U 5K5V 5K60 5K61 5K62 5K63 5K66
DescriptorNta1p, ASN-GLU-ALA (3 entities in total)
Functional Keywordsn-end rule, nitrilase superfamily, nta1, hydrolase
Biological sourceSaccharomyces cerevisiae (strain CEN.PK113-7D) (Baker's yeast)
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Total number of polymer chains2
Total molecular weight52382.15
Authors
Kim, M.K.,Oh, S.-J.,Lee, B.-G.,Song, H.K. (deposition date: 2016-05-24, release date: 2017-01-11)
Primary citation
Kim, M.K.,Oh, S.J.,Lee, B.G.,Song, H.K.
Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway.
Proc. Natl. Acad. Sci. U.S.A., 113:12438-12443, 2016
PubMed: 27791147 (PDB entries with the same primary citation)
DOI: 10.1073/pnas.1612620113
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.042 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.254140.2%00.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5b62
no rotation
Molmil generated image of 5b62
rotated about x axis by 90°
Molmil generated image of 5b62
rotated about y axis by 90°

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight52382.1
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight52382.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.042 Å)

Cell axes133.796133.796118.896
Cell angles90.0090.0090.00
SpacegroupI 41 2 2
Resolution limits33.04 - 3.04
the highest resolution shell value3.180 - 3.042
R-factor0.2107
R-work0.20590
the highest resolution shell value0.265
R-free0.25380
the highest resolution shell value0.313
RMSD bond length0.002
RMSD bond angle0.452

Data Collection Statistics

Resolution limits33.04 - 3.04
the highest resolution shell value -
Number of reflections10652
Completeness99.9
Redundancy13.2

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
A0016810molecular_functionhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
A0006807biological_processnitrogen compound metabolic process
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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

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Functional Information from PROSITE/UniProt

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Functional Information from SwissProt/UniProt

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Catalytic Information from CSA

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> Sequence Neighbor

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