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- PDB-6a0i: Crystal structure of human protein N-terminal asparagine amidohyd... -

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Basic information

Entry
Database: PDB / ID: 6a0i
TitleCrystal structure of human protein N-terminal asparagine amidohydrolase (NTAN1) C75S mutant
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: 1.996 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

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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)73,86727
Polymers71,5562
Non-polymers2,31125
Water7,963442
1
A: Protein N-terminal asparagine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,07315
Polymers35,7781
Non-polymers1,29514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein N-terminal asparagine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,79412
Polymers35,7781
Non-polymers1,01611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.982, 84.340, 86.998
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: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
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: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42029 / % possible obs: 100 % / Redundancy: 7.2 % / Rpim(I) all: 0.048 / Rsym value: 0.121 / Net I/σ(I): 16.31
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.8 % / Num. unique obs: 2075 / Rpim(I) all: 0.247 / Rsym value: 0.602 / % 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: 6A0E

6a0e


Resolution: 1.996→38.527 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 2003 4.77 %
Rwork0.164 --
obs0.1662 41963 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.996→38.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 147 442 5403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055125
X-RAY DIFFRACTIONf_angle_d0.7266932
X-RAY DIFFRACTIONf_dihedral_angle_d9.1914830
X-RAY DIFFRACTIONf_chiral_restr0.049755
X-RAY DIFFRACTIONf_plane_restr0.005904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.996-2.04590.24851450.18562612X-RAY DIFFRACTION92
2.0459-2.10120.28641280.19392837X-RAY DIFFRACTION100
2.1012-2.1630.23611400.17992849X-RAY DIFFRACTION100
2.163-2.23280.24061530.17562825X-RAY DIFFRACTION100
2.2328-2.31260.18951370.16552828X-RAY DIFFRACTION100
2.3126-2.40520.22991440.16962840X-RAY DIFFRACTION100
2.4052-2.51470.26451270.17412849X-RAY DIFFRACTION100
2.5147-2.64720.24471440.17762846X-RAY DIFFRACTION100
2.6472-2.8130.22521500.1762869X-RAY DIFFRACTION100
2.813-3.03010.21831390.17052858X-RAY DIFFRACTION100
3.0301-3.33490.21191460.1652883X-RAY DIFFRACTION100
3.3349-3.81710.17581530.14552879X-RAY DIFFRACTION100
3.8171-4.80770.15781410.13562934X-RAY DIFFRACTION100
4.8077-38.53380.23271560.17923051X-RAY DIFFRACTION100

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