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- PDB-6a0h: Crystal structure of human protein N-terminal asparagine amidohyd... -

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Basic information

Entry
Database: PDB / ID: 6a0h
TitleCrystal structure of human protein N-terminal asparagine amidohydrolase (NTAN1) C75S mutant with Asn-Leu-Ala-Ala-Arg peptide
Components
  • 5-mer peptide ASN-LEU-ALA-ALA-ARG
  • Protein N-terminal asparagine amidohydrolase
KeywordsHYDROLASE / Complex / Amidohydrolase
Function / homology
Function and homology information


protein N-terminal asparagine amidohydrolase / protein-N-terminal asparagine amidohydrolase activity / adult locomotory behavior / memory / ubiquitin-dependent protein catabolic process / nucleus / cytoplasm
Similarity search - Function
Protein N-terminal asparagine amidohydrolase / Protein N-terminal asparagine amidohydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Protein N-terminal asparagine amidohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.185 Å
AuthorsPark, J.S. / Han, B.W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2011-0030001 Korea, Republic Of
National Research Foundation (Korea)2013M-3A6A-4043695 Korea, Republic Of
CitationJournal: Biomolecules / Year: 2020
Title: Structural Analyses on the Deamidation of N-Terminal Asn in the Human N-Degron Pathway.
Authors: Park, J.S. / Lee, J.Y. / Nguyen, Y.T.K. / Kang, N.W. / Oh, E.K. / Jang, D.M. / Kim, H.J. / Kim, D.D. / Han, B.W.
History
DepositionJun 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein N-terminal asparagine amidohydrolase
B: Protein N-terminal asparagine amidohydrolase
C: 5-mer peptide ASN-LEU-ALA-ALA-ARG
D: 5-mer peptide ASN-LEU-ALA-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,67615
Polymers72,6464
Non-polymers1,03011
Water23413
1
A: Protein N-terminal asparagine amidohydrolase
C: 5-mer peptide ASN-LEU-ALA-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8848
Polymers36,3232
Non-polymers5616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-27 kcal/mol
Surface area14270 Å2
MethodPISA
2
B: Protein N-terminal asparagine amidohydrolase
D: 5-mer peptide ASN-LEU-ALA-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7927
Polymers36,3232
Non-polymers4695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-29 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.003, 85.884, 88.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein N-terminal asparagine amidohydrolase / Protein NH2-terminal asparagine amidohydrolase / PNAA / Protein NH2-terminal asparagine deamidase / ...Protein NH2-terminal asparagine amidohydrolase / PNAA / Protein NH2-terminal asparagine deamidase / Protein NTN-amidase


Mass: 35778.227 Da / Num. of mol.: 2 / Mutation: C75S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTAN1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q96AB6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide 5-mer peptide ASN-LEU-ALA-ALA-ARG


Mass: 544.625 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.8 / Details: PEG 4000, potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 11141 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 47.35 Å2 / Rpim(I) all: 0.067 / Rsym value: 0.172 / Net I/σ(I): 9.67
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 7.9 % / Num. unique obs: 552 / Rpim(I) all: 0.182 / Rsym value: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A0I

6a0i


Resolution: 3.185→35.517 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 541 4.87 %
Rwork0.185 --
obs0.1878 11098 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.185→35.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 60 13 4895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024974
X-RAY DIFFRACTIONf_angle_d0.5096738
X-RAY DIFFRACTIONf_dihedral_angle_d12.0562995
X-RAY DIFFRACTIONf_chiral_restr0.04749
X-RAY DIFFRACTIONf_plane_restr0.005878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1851-3.50540.30361300.21212590X-RAY DIFFRACTION100
3.5054-4.0120.2471410.18782595X-RAY DIFFRACTION100
4.012-5.05240.23651290.16012626X-RAY DIFFRACTION100
5.0524-35.51960.21481410.19272746X-RAY DIFFRACTION100

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