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- PDB-6zeq: Aspergillus oryzae Leucine Aminopeptidase A mature enzyme -

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Basic information

Entry
Database: PDB / ID: 6zeq
TitleAspergillus oryzae Leucine Aminopeptidase A mature enzyme
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 aminopeptidase A
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
DepositionJun 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine aminopeptidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,66316
Polymers41,1521
Non-polymers1,51115
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-145 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.920, 153.920, 88.640
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-407-

SO4

21A-580-

HOH

31A-589-

HOH

41A-739-

HOH

51A-761-

HOH

61A-830-

HOH

71A-835-

HOH

81A-920-

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: 41151.719 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) / Variant (production host): X33
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 , 5 types, 476 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Citrate, pH = 5.0, 3.2 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.97→73.81 Å / Num. obs: 43994 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.2203 / Net I/σ(I): 10.35
Reflection shellResolution: 1.97→2.041 Å / Rmerge(I) obs: 2.178 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 4297 / CC1/2: 0.653 / CC star: 0.889

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTQ

1rtq


Resolution: 1.97→73.81 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 2125 4.83 %
Rwork0.1645 41867 -
obs0.1664 43992 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.36 Å2 / Biso mean: 37.8875 Å2 / Biso min: 19.83 Å2
Refinement stepCycle: final / Resolution: 1.97→73.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 82 462 2848
Biso mean--61.49 51.15 -
Num. residues----301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.020.4161380.34872733287199
2.02-2.070.38091220.31232758288099
2.07-2.120.35741160.29392733284999
2.12-2.180.31141230.27827442867100
2.18-2.260.27481440.251427602904100
2.26-2.340.2781370.227827642901100
2.34-2.430.27261440.217227382882100
2.43-2.540.23631490.197927722921100
2.54-2.670.21751590.18527612920100
2.67-2.840.23671540.181127662920100
2.84-3.060.2281480.169127902938100
3.06-3.370.19691450.146727992944100
3.37-3.860.16151600.120328332993100
3.86-4.860.12451490.101528563005100
4.86-73.810.16371370.130530603197100

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