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- PDB-6a0f: Crystal structure of human protein N-terminal asparagine amidohyd... -

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Basic information

Entry
Database: PDB / ID: 6a0f
TitleCrystal structure of human protein N-terminal asparagine amidohydrolase (NTAN1) C75S mutant with Asn-Phe-Ala-Ala-Arg peptide
Components
  • 5-mer peptide Asn-Phe-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: 2.384 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein N-terminal asparagine amidohydrolase
B: Protein N-terminal asparagine amidohydrolase
C: 5-mer peptide Asn-Phe-Ala-Ala-Arg
D: 5-mer peptide Asn-Phe-Ala-Ala-Arg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,67125
Polymers72,7144
Non-polymers1,95721
Water3,927218
1
A: Protein N-terminal asparagine amidohydrolase
C: 5-mer peptide Asn-Phe-Ala-Ala-Arg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,66116
Polymers36,3572
Non-polymers1,30414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-39 kcal/mol
Surface area13920 Å2
MethodPISA
2
B: Protein N-terminal asparagine amidohydrolase
D: 5-mer peptide Asn-Phe-Ala-Ala-Arg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0109
Polymers36,3572
Non-polymers6537
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-26 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.045, 85.749, 88.297
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-Phe-Ala-Ala-Arg


Mass: 578.641 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


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 43.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: PEG 3350, 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: 2.4→50 Å / Num. obs: 25940 / % possible obs: 99.9 % / Redundancy: 7.8 % / Rpim(I) all: 0.035 / Rsym value: 0.092 / Net I/σ(I): 18.41
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 1246 / Rpim(I) all: 0.19 / Rsym value: 0.502

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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: 2.384→30.757 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1317 5.09 %
Rwork0.1956 --
obs0.1982 25887 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.384→30.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4857 0 118 218 5193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025060
X-RAY DIFFRACTIONf_angle_d0.4646844
X-RAY DIFFRACTIONf_dihedral_angle_d13.7213029
X-RAY DIFFRACTIONf_chiral_restr0.04751
X-RAY DIFFRACTIONf_plane_restr0.004887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3835-2.47890.35181370.27642537X-RAY DIFFRACTION93
2.4789-2.59170.33781420.24362695X-RAY DIFFRACTION100
2.5917-2.72820.32681430.23892721X-RAY DIFFRACTION100
2.7282-2.8990.25791510.2382697X-RAY DIFFRACTION100
2.899-3.12270.31791450.22332735X-RAY DIFFRACTION100
3.1227-3.43660.25461470.20522747X-RAY DIFFRACTION100
3.4366-3.9330.22521530.17052749X-RAY DIFFRACTION100
3.933-4.95180.18691450.14952789X-RAY DIFFRACTION100
4.9518-30.75990.22011540.19022900X-RAY DIFFRACTION99

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