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- PDB-6a0e: Crystal structure of human protein N-terminal asparagine amidohyd... -

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Basic information

Entry
Database: PDB / ID: 6a0e
TitleCrystal structure of human protein N-terminal asparagine amidohydrolase (NTAN1)
ComponentsProtein N-terminal asparagine amidohydrolase
KeywordsHYDROLASE / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.947 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 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Protein N-terminal asparagine amidohydrolase
B: Protein N-terminal asparagine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1448
Polymers71,5892
Non-polymers5556
Water10,683593
1
A: Protein N-terminal asparagine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1665
Polymers35,7941
Non-polymers3714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-6 kcal/mol
Surface area14520 Å2
MethodPISA
2
B: Protein N-terminal asparagine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9783
Polymers35,7941
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.153, 84.903, 87.198
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: 35794.293 Da / Num. of mol.: 2
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.15 Å3/Da / Density % sol: 42.79 % / Description: Rod-shaped
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: PEG 3350, Potassium phosphate monobasic / Temp details: incubator

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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: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 45885 / % possible obs: 100 % / Redundancy: 7.3 % / Rpim(I) all: 0.037 / Rsym value: 0.091 / Net I/σ(I): 21.18
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.3 % / Num. unique obs: 2264 / Rpim(I) all: 0.276 / Rsym value: 0.701 / % 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 / Resolution: 1.947→30.415 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 1996 4.36 %
Rwork0.1745 --
obs0.1766 45810 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.947→30.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 35 593 5442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025141
X-RAY DIFFRACTIONf_angle_d0.4896999
X-RAY DIFFRACTIONf_dihedral_angle_d16.1933121
X-RAY DIFFRACTIONf_chiral_restr0.042768
X-RAY DIFFRACTIONf_plane_restr0.003936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9471-1.99580.26451380.20483044X-RAY DIFFRACTION99
1.9958-2.04970.27081430.19523085X-RAY DIFFRACTION100
2.0497-2.110.26181470.2023100X-RAY DIFFRACTION100
2.11-2.17810.24441410.18813087X-RAY DIFFRACTION100
2.1781-2.25590.23771300.18173095X-RAY DIFFRACTION100
2.2559-2.34620.22631430.18243103X-RAY DIFFRACTION100
2.3462-2.4530.26621430.18913127X-RAY DIFFRACTION100
2.453-2.58220.23241410.1833110X-RAY DIFFRACTION100
2.5822-2.74390.26971450.18253108X-RAY DIFFRACTION100
2.7439-2.95560.23671440.1863126X-RAY DIFFRACTION100
2.9556-3.25270.24241330.17383145X-RAY DIFFRACTION100
3.2527-3.72270.18471460.16233169X-RAY DIFFRACTION100
3.7227-4.68740.16951430.14073194X-RAY DIFFRACTION100
4.6874-30.4190.23491590.18353321X-RAY DIFFRACTION100

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