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- PDB-6lko: Turning an asparaginyl endopeptidase into a peptide ligase -

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Basic information

Entry
Database: PDB / ID: 6lko
TitleTurning an asparaginyl endopeptidase into a peptide ligase
ComponentsAsparaginyl endopeptidase
KeywordsHYDROLASE / AEP / Asparaginyl Endopeptidase / Peptide asparaginyl Ligase / PAL
Function / homology
Function and homology information


legumain / vacuolar protein processing / vacuole / proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity
Similarity search - Function
Asparaginyl endopeptidase / Legumain prodomain superfamily / : / Legumain, prodomain / Peptidase C13, legumain / Peptidase C13 family
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Asparaginyl endopeptidase
Similarity search - Component
Biological speciesClitoria ternatea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEl Sahili, A. / Lescar, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2016-T3-1-003 Singapore
CitationJournal: Acs Catalysis / Year: 2020
Title: Turning an Asparaginyl Endopeptidase into a Peptide Ligase
Authors: Hemu, X. / El Sahili, A. / Hu, S. / Zhang, X. / Serra, A. / Goh, B.C. / Darwis, D.A. / Chen, M.W. / Sze, S.K. / Liu, C.F. / Lescar, J. / Tam, J.P.
History
DepositionDec 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 9, 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: Asparaginyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1173
Polymers55,7901
Non-polymers3272
Water5,188288
1
A: Asparaginyl endopeptidase
hetero molecules

A: Asparaginyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2346
Polymers111,5802
Non-polymers6554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area2720 Å2
ΔGint-7 kcal/mol
Surface area31850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.550, 79.740, 135.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Asparaginyl endopeptidase


Mass: 55789.918 Da / Num. of mol.: 1 / Mutation: P183A, G252V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clitoria ternatea (plant) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0P0QM28, legumain
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% v/v PEG 500* MME, 10 % w/v PEG 20000, 0.1M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate tetrahydrate, 0.1M Sodium ...Details: 20% v/v PEG 500* MME, 10 % w/v PEG 20000, 0.1M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1M Sodium HEPES, MOPS (acid)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2→42.31 Å / Num. obs: 60392 / % possible obs: 99.96 % / Redundancy: 13 % / Biso Wilson estimate: 32.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.093 / Net I/σ(I): 22.66
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 1.076 / Num. unique obs: 3230 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L4V

6l4v


Resolution: 2→42.31 Å / SU ML: 0.2248 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 21.3534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2052 3019 5 %
Rwork0.1932 57373 -
obs0.1938 60392 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.4 Å2
Refinement stepCycle: LAST / Resolution: 2→42.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 21 288 3516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01293319
X-RAY DIFFRACTIONf_angle_d1.34284486
X-RAY DIFFRACTIONf_chiral_restr0.0951481
X-RAY DIFFRACTIONf_plane_restr0.0075584
X-RAY DIFFRACTIONf_dihedral_angle_d17.85991211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.30711400.26932683X-RAY DIFFRACTION97.65
2.03-2.060.27021400.25162687X-RAY DIFFRACTION100
2.06-2.10.23521430.24432699X-RAY DIFFRACTION100
2.1-2.140.27481440.22572728X-RAY DIFFRACTION100
2.14-2.180.29461430.24512698X-RAY DIFFRACTION100
2.18-2.220.44611160.40132240X-RAY DIFFRACTION88.24
2.23-2.270.651610.5991161X-RAY DIFFRACTION45.68
2.27-2.330.29841380.28252642X-RAY DIFFRACTION96.83
2.33-2.380.23491350.19732693X-RAY DIFFRACTION99.96
2.38-2.450.20681400.20082718X-RAY DIFFRACTION100
2.45-2.520.22211430.20342693X-RAY DIFFRACTION99.96
2.52-2.60.21361460.1892750X-RAY DIFFRACTION100
2.6-2.690.27521430.19312677X-RAY DIFFRACTION99.96
2.69-2.80.25821390.19742727X-RAY DIFFRACTION100
2.8-2.930.20751410.19942715X-RAY DIFFRACTION100
2.93-3.080.21041470.1932685X-RAY DIFFRACTION99.96
3.08-3.280.18951440.18352719X-RAY DIFFRACTION100
3.28-3.530.18221380.17362723X-RAY DIFFRACTION99.97
3.53-3.880.16231370.17692616X-RAY DIFFRACTION96.87
3.89-4.450.15821500.1412718X-RAY DIFFRACTION99.79
4.45-5.60.13261490.14632694X-RAY DIFFRACTION99.93
5.6-42.310.17291420.17592707X-RAY DIFFRACTION99.75

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