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- PDB-5k63: Crystal structure of N-terminal amidase C187S -

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Basic information

Entry
Database: PDB / ID: 5k63
TitleCrystal structure of N-terminal amidase C187S
ComponentsNta1p
KeywordsHYDROLASE / N-end rule / Nitrilase superfamily / Nta1
Function / homology
Function and homology information


protein-N-terminal glutamine amidohydrolase activity / protein-N-terminal asparagine amidohydrolase activity / protein catabolic process / protein modification process
Similarity search - Function
Protein N-terminal amidase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
ASPARAGINE / GLYCINE / Nta1p
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nta1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2573
Polymers52,0501
Non-polymers2072
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.355, 134.355, 119.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-683-

HOH

21A-684-

HOH

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Components

#1: Protein Nta1p


Mass: 52049.840 Da / Num. of mol.: 1 / Mutation: C187S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain CEN.PK113-7D) (yeast)
Strain: CEN.PK113-7D / Gene: CENPK1137D_1355 / Production host: Escherichia coli (E. coli) / References: UniProt: N1P8Q8
#2: Chemical ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O3
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
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: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→38.276 Å / Num. obs: 19185 / % possible obs: 99.9 % / Redundancy: 15.2 % / Net I/σ(I): 56.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.5→38.276 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.86
RfactorNum. reflection% reflection
Rfree0.2468 1919 10 %
Rwork0.185 --
obs0.1909 19185 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→38.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 0 86 3432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053420
X-RAY DIFFRACTIONf_angle_d0.8664638
X-RAY DIFFRACTIONf_dihedral_angle_d11.0611217
X-RAY DIFFRACTIONf_chiral_restr0.032521
X-RAY DIFFRACTIONf_plane_restr0.004594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4999-2.56240.3331280.23331153X-RAY DIFFRACTION96
2.5624-2.63170.31591350.23731221X-RAY DIFFRACTION100
2.6317-2.70910.31481340.22631199X-RAY DIFFRACTION100
2.7091-2.79650.31041370.21621232X-RAY DIFFRACTION100
2.7965-2.89640.29181360.22981221X-RAY DIFFRACTION100
2.8964-3.01230.24531350.22231218X-RAY DIFFRACTION100
3.0123-3.14940.26411370.21521228X-RAY DIFFRACTION100
3.1494-3.31530.2391350.20721226X-RAY DIFFRACTION100
3.3153-3.52290.32161390.19881243X-RAY DIFFRACTION100
3.5229-3.79470.23011360.18491228X-RAY DIFFRACTION100
3.7947-4.17610.2071390.16521243X-RAY DIFFRACTION100
4.1761-4.77950.22511380.14261254X-RAY DIFFRACTION100
4.7795-6.01780.19621420.15811269X-RAY DIFFRACTION100
6.0178-38.28050.23561480.17781331X-RAY DIFFRACTION99

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