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- PDB-6zep: Flavourzyme Leucine Aminopeptidase A proenzyme -

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Basic information

Entry
Database: PDB / ID: 6zep
TitleFlavourzyme Leucine Aminopeptidase A proenzyme
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 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Leucine aminopeptidase A
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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

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Assembly

Deposited unit
A: Leucine aminopeptidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7776
Polymers41,1521
Non-polymers1,6265
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-67 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.430, 94.390, 99.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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)
Gene: lapA, AO090011000052 / Production host: Komagataella pastoris (fungus) / Variant (production host): X33
References: UniProt: Q2U1F3, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 486 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris, pH = 5.5, 0.2 M NaCl, 25% PEG 3,350

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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: 1.61→42.611 Å / Num. obs: 53338 / % possible obs: 99.48 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.07303 / Net I/σ(I): 11.36
Reflection shellResolution: 1.61→1.668 Å / Rmerge(I) obs: 0.8915 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 5269 / CC1/2: 0.55 / CC star: 0.842 / Rrim(I) all: 0.08292

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTQ

1rtq


Resolution: 1.61→42.611 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.16
RfactorNum. reflection% reflection
Rfree0.1739 2671 5.01 %
Rwork0.1527 --
obs0.1537 53338 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.61→42.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 101 482 3201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072869
X-RAY DIFFRACTIONf_angle_d0.933910
X-RAY DIFFRACTIONf_dihedral_angle_d15.0091726
X-RAY DIFFRACTIONf_chiral_restr0.057450
X-RAY DIFFRACTIONf_plane_restr0.006502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.63930.31311390.3042604X-RAY DIFFRACTION100
1.6393-1.67080.27711460.27652666X-RAY DIFFRACTION100
1.6708-1.70490.29451470.26242591X-RAY DIFFRACTION100
1.7049-1.7420.26911710.23022618X-RAY DIFFRACTION100
1.742-1.78250.23311630.21722609X-RAY DIFFRACTION100
1.7825-1.82710.20441310.19612656X-RAY DIFFRACTION100
1.8271-1.87650.22541370.18482643X-RAY DIFFRACTION100
1.8765-1.93170.20351300.18442651X-RAY DIFFRACTION100
1.9317-1.99410.21611270.17662678X-RAY DIFFRACTION100
1.9941-2.06530.19791170.16962634X-RAY DIFFRACTION98
2.0653-2.1480.20611390.15182667X-RAY DIFFRACTION100
2.148-2.24580.17881430.1472666X-RAY DIFFRACTION100
2.2458-2.36420.17311210.14142696X-RAY DIFFRACTION100
2.3642-2.51230.17631130.14372686X-RAY DIFFRACTION100
2.5123-2.70620.16181580.14132657X-RAY DIFFRACTION99
2.7062-2.97850.18121240.14512705X-RAY DIFFRACTION100
2.9785-3.40930.16961480.13472698X-RAY DIFFRACTION100
3.4093-4.29470.12311610.11822699X-RAY DIFFRACTION98
4.2947-42.6110.13611560.13512843X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.4382 Å / Origin y: -2.2698 Å / Origin z: 9.909 Å
111213212223313233
T0.1076 Å2-0.0002 Å2-0.0007 Å2-0.1126 Å20.0089 Å2--0.1336 Å2
L0.975 °20.2036 °20.1458 °2-0.8144 °20.2231 °2--1.3686 °2
S-0.0181 Å °0.0085 Å °0.0229 Å °0.0202 Å °0.003 Å °0.0355 Å °-0.014 Å °-0.0538 Å °0.0091 Å °
Refinement TLS groupSelection details: all

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