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- PDB-8jkt: Crystal structure of feline aminopeptidase N ectodomain -

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Basic information

Entry
Database: PDB / ID: 8jkt
TitleCrystal structure of feline aminopeptidase N ectodomain
ComponentsAminopeptidase N
KeywordsHYDROLASE / aminopeptidase / viral receptor / coronaviruses
Function / homology
Function and homology information


membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / proteolysis / extracellular space / zinc ion binding ...membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / proteolysis / extracellular space / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Biological speciesFelis catus (domestic cat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTan, Y.B. / Shi, Y.J. / Peng, G.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of feline aminopeptidase N ectodomain
Authors: Tan, Y.B. / Shi, Y.J. / Peng, G.Q.
History
DepositionJun 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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: Aminopeptidase N
B: Aminopeptidase N
C: Aminopeptidase N
D: Aminopeptidase N


Theoretical massNumber of molelcules
Total (without water)443,6654
Polymers443,6654
Non-polymers00
Water69,1783840
1
A: Aminopeptidase N
C: Aminopeptidase N


Theoretical massNumber of molelcules
Total (without water)221,8322
Polymers221,8322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase N
D: Aminopeptidase N


Theoretical massNumber of molelcules
Total (without water)221,8322
Polymers221,8322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.200, 132.588, 129.364
Angle α, β, γ (deg.)90.00, 101.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aminopeptidase N / AP-N / fAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase


Mass: 110916.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: ANPEP, APN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P79171, membrane alanyl aminopeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3840 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium Thiocyanate pH 6.9, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97835 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97835 Å / Relative weight: 1
ReflectionResolution: 1.9→35.83 Å / Num. obs: 318333 / % possible obs: 99.89 % / Redundancy: 6.7 % / CC1/2: 0.996 / Net I/σ(I): 18.3
Reflection shellResolution: 1.9→5.16 Å / Num. unique obs: 17090 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.83 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 2014 0.63 %
Rwork0.1777 --
obs0.178 318333 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→35.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29054 0 0 3840 32894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00929838
X-RAY DIFFRACTIONf_angle_d1.20940699
X-RAY DIFFRACTIONf_dihedral_angle_d6.5153885
X-RAY DIFFRACTIONf_chiral_restr0.0714517
X-RAY DIFFRACTIONf_plane_restr0.0125204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.26981300.228222353X-RAY DIFFRACTION99
1.95-20.26041550.21322501X-RAY DIFFRACTION100
2-2.060.25011410.205422581X-RAY DIFFRACTION100
2.06-2.130.26481480.201722543X-RAY DIFFRACTION100
2.13-2.20.25291390.191722562X-RAY DIFFRACTION100
2.2-2.290.23341420.188822565X-RAY DIFFRACTION100
2.29-2.40.23411460.184622533X-RAY DIFFRACTION100
2.4-2.520.22171450.182122580X-RAY DIFFRACTION100
2.52-2.680.22171420.179822596X-RAY DIFFRACTION100
2.68-2.890.26051470.182522588X-RAY DIFFRACTION100
2.89-3.180.20871410.182822643X-RAY DIFFRACTION100
3.18-3.640.20011470.165622682X-RAY DIFFRACTION100
3.64-4.580.17381430.147822702X-RAY DIFFRACTION100
4.58-35.830.2161480.167922890X-RAY DIFFRACTION100

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