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- PDB-6l4w: Turning an asparaginyl endopeptidase into a peptide ligase -

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Basic information

Entry
Database: PDB / ID: 6l4w
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: 1.66 Å
AuthorsEl Sahili, A. / Lescar, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (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
DepositionOct 21, 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_rmsd_angle / 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 16, 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)56,2054
Polymers55,8161
Non-polymers3893
Water7,062392
1
A: Asparaginyl endopeptidase
hetero molecules

A: Asparaginyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4118
Polymers111,6322
Non-polymers7796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2890 Å2
ΔGint-4 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.150, 135.590, 44.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Asparaginyl endopeptidase / Butelase 2A


Mass: 55815.953 Da / Num. of mol.: 1 / Mutation: G252V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clitoria ternatea (plant)
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.2
Details: 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 HEPES, 0.1M MOPS, 10% Ethylen Glycol, 8% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91882 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91882 Å / Relative weight: 1
ReflectionResolution: 1.66→22.79 Å / Num. obs: 56975 / % possible obs: 98.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.07842 / Net I/σ(I): 13.9
Reflection shellResolution: 1.66→1.72 Å / Rmerge(I) obs: 1.722

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L4V

6l4v


Resolution: 1.66→22.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 2821 -RANDOM
Rwork0.2062 ---
obs0.2076 56398 98.6 %-
Displacement parametersBiso mean: 32.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.1485 Å20 Å20 Å2
2--1.1838 Å20 Å2
3----2.3324 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.66→22.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 2287 392 3616
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083325HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.964495HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1145SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes565HARMONIC5
X-RAY DIFFRACTIONt_it3325HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion16.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion417SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3355SEMIHARMONIC4
LS refinement shellResolution: 1.66→1.72 Å
RfactorNum. reflection% reflection
Rfree0.4279 57 -
Rwork0.3242 --
obs--84.97 %

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