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- PDB-6l4y: Turning an asparaginyl endopeptidase into a peptide ligase -

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Basic information

Entry
Database: PDB / ID: 6l4y
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 / proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity
Similarity search - Function
: / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / 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: 1.5 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
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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Asparaginyl endopeptidase
B: Asparaginyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2796
Polymers111,6682
Non-polymers6114
Water16,123895
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-4 kcal/mol
Surface area32700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.61, 79.6, 136.47
Angle α, β, γ (deg.)90, 93.95, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Asparaginyl endopeptidase


Mass: 55833.969 Da / Num. of mol.: 2 / Mutation: E74V,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.: 2
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.: 895 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.26 %
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: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953736 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953736 Å / Relative weight: 1
ReflectionResolution: 1.5→21.84 Å / Num. obs: 151957 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 24.33 Å2 / Rmerge(I) obs: 0.0569 / Net I/σ(I): 11.01
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 1.055 / Num. unique obs: 15107

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L4V

6l4v


Resolution: 1.5→21.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.063
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 7598 -RANDOM
Rwork0.1715 ---
obs0.1724 151957 99.9 %-
Displacement parametersBiso mean: 30.83 Å2
Baniso -1Baniso -2Baniso -3
1--2.8293 Å20 Å2-0.4089 Å2
2--1.1732 Å20 Å2
3---1.656 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.5→21.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 4638 895 7403
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096795HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.969219HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2338SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1167HARMONIC5
X-RAY DIFFRACTIONt_it6795HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion843SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7132SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion15.29
LS refinement shellResolution: 1.5→1.51 Å
RfactorNum. reflection% reflection
Rfree0.2494 152 -
Rwork0.2618 --
obs0.2612 3040 99.8 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.03190.02210.02680.2356-0.03180.2585-0.01110.05250.00840.0525-0.0009-0.01560.0084-0.01560.0119-0.06060.0054-0.0078-0.01980.0019-0.0289-2.62725.6092146.7486
20.017-0.0013-0.02930.3937-0.02770.26450.0001-0.0291-0.0168-0.0291-0.0023-0.0393-0.0168-0.03930.0022-0.0504-0.0021-0.0092-0.03520.0007-0.0248-5.9507-12.0631194.5643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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