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- PDB-5jgf: Crystal structure of mApe1 -

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Basic information

Entry
Database: PDB / ID: 5jgf
TitleCrystal structure of mApe1
ComponentsVacuolar aminopeptidase 1
KeywordsHYDROLASE / tetrahedral dodecamer
Function / homology
Function and homology information


aminopeptidase I / Cvt complex / cytoplasm to vacuole targeting by the Cvt pathway / fungal-type vacuole / metalloaminopeptidase activity / proteolysis / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Aminopeptidase i, Domain 2 / Aminopeptidase i, Domain 2 / Peptidase M18 / Peptidase M18, domain 2 / Aminopeptidase I zinc metalloprotease (M18) / Zn peptidases / Aminopeptidase / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Vacuolar aminopeptidase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsNoda, N.N. / Adachi, W. / Inagaki, F.
CitationJournal: Cell Rep / Year: 2016
Title: Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates
Authors: Yamasaki, A. / Watanabe, Y. / Adachi, W. / Suzuki, K. / Matoba, K. / Kirisako, H. / Kumeta, H. / Nakatogawa, H. / Ohsumi, Y. / Inagaki, F. / Noda, N.N.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Derived calculations
Revision 1.3Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar aminopeptidase 1
B: Vacuolar aminopeptidase 1
C: Vacuolar aminopeptidase 1
D: Vacuolar aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,23912
Polymers208,7154
Non-polymers5238
Water43,2542401
1
A: Vacuolar aminopeptidase 1
B: Vacuolar aminopeptidase 1
C: Vacuolar aminopeptidase 1
D: Vacuolar aminopeptidase 1
hetero molecules

A: Vacuolar aminopeptidase 1
B: Vacuolar aminopeptidase 1
C: Vacuolar aminopeptidase 1
D: Vacuolar aminopeptidase 1
hetero molecules

A: Vacuolar aminopeptidase 1
B: Vacuolar aminopeptidase 1
C: Vacuolar aminopeptidase 1
D: Vacuolar aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)627,71636
Polymers626,14612
Non-polymers1,57024
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area81340 Å2
ΔGint-1263 kcal/mol
Surface area162050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.969, 140.969, 348.917
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11C-1286-

HOH

21C-1312-

HOH

31D-715-

HOH

41D-1187-

HOH

51D-1225-

HOH

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Components

#1: Protein
Vacuolar aminopeptidase 1 / Aminopeptidase yscI / Leucine aminopeptidase IV / LAPIV / Lysosomal aminopeptidase III / ...Aminopeptidase yscI / Leucine aminopeptidase IV / LAPIV / Lysosomal aminopeptidase III / Polypeptidase / Vacuolar aminopeptidase I


Mass: 52178.828 Da / Num. of mol.: 4 / Fragment: UNP residues 46-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: APE1, API, LAP4, YSC1, YKL103C, YKL455 / Production host: Escherichia coli (E. coli) / References: UniProt: P14904, aminopeptidase I
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2401 / 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: 3.2 Å3/Da / Density % sol: 61.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Tris-HCl, 30% polyethylene glycol 400, 0.1 M MgCl2, 1.1 M NaCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.83→100 Å / Num. obs: 227735 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.8 Å2 / Net I/σ(I): 27.1
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y7E

1y7e


Resolution: 1.83→38.49 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 135829.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.179 22019 10 %RANDOM
Rwork0.162 ---
obs0.162 220277 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.4511 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.83→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14181 0 8 2401 16590
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 1.83→1.94 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 3500 10.1 %
Rwork0.206 31252 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION3CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top

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