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- PDB-5k5u: Crystal structure of N-terminal amidase -

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Basic information

Entry
Database: PDB / ID: 5k5u
TitleCrystal structure of N-terminal amidase
ComponentsNta1p
KeywordsHYDROLASE / N-end rule / Nitrilase superfamily / Nta1
Function / homologyProtein N-terminal amidase / protein-N-terminal glutamine amidohydrolase activity / protein-N-terminal asparagine amidohydrolase activity / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / Nta1p
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsKim, M.K. / Oh, S.-J. / Lee, B.-G. / Song, H.K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway.
Authors: Kim, M.K. / Oh, S.J. / Lee, B.G. / Song, H.K.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nta1p


Theoretical massNumber of molelcules
Total (without water)52,0661
Polymers52,0661
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.680, 133.680, 119.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Nta1p


Mass: 52065.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae / Strain: CEN.PK113-7D / Gene: CENPK1137D_1355 / Production host: Escherichia coli (E. coli) / References: UniProt: N1P8Q8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Mg acetate tetrahydrate, 0.2M Na cacodylate pH6.5, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→29.9 Å / Num. obs: 14836 / % possible obs: 99.9 % / Redundancy: 16.1 % / Net I/σ(I): 63

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementResolution: 2.7→29.892 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 0.19 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 1482 9.99 %
Rwork0.2091 --
obs0.2148 14836 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 0 92 3422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023405
X-RAY DIFFRACTIONf_angle_d0.6324619
X-RAY DIFFRACTIONf_dihedral_angle_d10.8351223
X-RAY DIFFRACTIONf_chiral_restr0.027516
X-RAY DIFFRACTIONf_plane_restr0.004594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78710.35911310.26031159X-RAY DIFFRACTION95
2.7871-2.88670.33281300.26061131X-RAY DIFFRACTION94
2.8867-3.00210.28351270.24971168X-RAY DIFFRACTION96
3.0021-3.13860.35431340.25411195X-RAY DIFFRACTION98
3.1386-3.30390.28451320.24151203X-RAY DIFFRACTION99
3.3039-3.51060.28751360.21921229X-RAY DIFFRACTION99
3.5106-3.78120.26061350.20631217X-RAY DIFFRACTION100
3.7812-4.16080.25121370.18411226X-RAY DIFFRACTION99
4.1608-4.76080.21621360.16961241X-RAY DIFFRACTION99
4.7608-5.99020.21691370.18961257X-RAY DIFFRACTION100
5.9902-29.89360.27231470.20961328X-RAY DIFFRACTION99

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