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- PDB-7oez: Leucine Aminopeptidase A mature enzyme in a complex with leucine -

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Basic information

Entry
Database: PDB / ID: 7oez
TitleLeucine Aminopeptidase A mature enzyme in a complex with leucine
ComponentsLeucine aminopeptidase A
KeywordsHYDROLASE / M28 peptidase / prodomain / intramolecular chaperone / bimetallic aminopeptidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M28 family / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
LEUCINE / Leucine aminopeptidase A
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsWatson, K.A. / Baltulionis, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/K012053/1 United Kingdom
CitationJournal: J.Struct.Biol. / Year: 2021
Title: The role of propeptide-mediated autoinhibition and intermolecular chaperone in the maturation of cognate catalytic domain in leucine aminopeptidase.
Authors: Baltulionis, G. / Blight, M. / Robin, A. / Charalampopoulos, D. / Watson, K.A.
History
DepositionMay 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Leucine aminopeptidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,29316
Polymers32,7801
Non-polymers1,51315
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-49 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.100, 154.100, 87.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-403-

SO4

21A-404-

SO4

31A-404-

SO4

41A-408-

CL

51A-510-

HOH

61A-710-

HOH

71A-754-

HOH

81A-761-

HOH

91A-790-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Leucine aminopeptidase A / Leucyl aminopeptidase A / LAPA


Mass: 32780.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (strain ATCC 42149 / RIB 40) (mold)
Strain: ATCC 42149 / RIB 40 / Gene: lapA, AO090011000052 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q2U1F3, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 374 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.59 Å3/Da / Density % sol: 73.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Citrate, pH =5.0, 3.2M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.48→77.05 Å / Num. obs: 22302 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 35.33 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.09705 / Net I/σ(I): 7.08
Reflection shellResolution: 2.48→2.569 Å / Rmerge(I) obs: 0.4829 / Num. unique obs: 2195 / CC1/2: 0.556

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
APEXdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTQ

1rtq


Resolution: 2.48→77.05 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 1112 4.99 %
Rwork0.1567 21187 -
obs0.1595 22299 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.15 Å2 / Biso mean: 41.2881 Å2 / Biso min: 12.41 Å2
Refinement stepCycle: final / Resolution: 2.48→77.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 85 360 2750
Biso mean--76.36 49.66 -
Num. residues----301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.48-2.590.34171370.28225882725
2.59-2.730.30641230.264526062729
2.73-2.90.32691460.254125932739
2.9-3.120.26131540.192525892743
3.12-3.440.2341380.15426252763
3.44-3.940.16571420.118126442786
3.94-4.960.14161290.094126922821
4.96-77.050.18271430.136228502993

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