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- PDB-5k61: Crystal structure of N-terminal amidase with Gln-Gly peptide -

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Basic information

Entry
Database: PDB / ID: 5k61
TitleCrystal structure of N-terminal amidase with Gln-Gly peptide
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 domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.001 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 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1962
Polymers52,0501
Non-polymers1461
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.598, 133.598, 119.123
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-820-

HOH

21A-830-

HOH

31A-835-

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-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
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→33.4 Å / Num. obs: 36454 / % possible obs: 99.9 % / Redundancy: 15.7 % / Net I/σ(I): 66

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.001→33.399 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 22.99
RfactorNum. reflection% reflection
Rfree0.2146 2000 5.49 %
Rwork0.188 --
obs0.1895 36454 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→33.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 0 243 3592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073423
X-RAY DIFFRACTIONf_angle_d1.0294639
X-RAY DIFFRACTIONf_dihedral_angle_d12.7891224
X-RAY DIFFRACTIONf_chiral_restr0.041522
X-RAY DIFFRACTIONf_plane_restr0.005591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0011-2.05120.29141390.24282412X-RAY DIFFRACTION99
2.0512-2.10660.29021420.22932430X-RAY DIFFRACTION100
2.1066-2.16860.29021400.23592406X-RAY DIFFRACTION100
2.1686-2.23860.25511420.2192450X-RAY DIFFRACTION100
2.2386-2.31860.23421410.21672426X-RAY DIFFRACTION100
2.3186-2.41140.25011410.20532431X-RAY DIFFRACTION100
2.4114-2.52110.22051420.20542455X-RAY DIFFRACTION100
2.5211-2.65390.23151430.20222449X-RAY DIFFRACTION100
2.6539-2.82010.23581410.19522448X-RAY DIFFRACTION100
2.8201-3.03770.23551440.20292467X-RAY DIFFRACTION100
3.0377-3.34320.20681430.1952460X-RAY DIFFRACTION100
3.3432-3.82640.19771440.17912496X-RAY DIFFRACTION100
3.8264-4.81850.16941460.14962512X-RAY DIFFRACTION100
4.8185-33.40410.20411520.17842612X-RAY DIFFRACTION99

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