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- PDB-6l4x: Turning an asparaginyl endopeptidase into a peptide ligase -

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Basic information

Entry
Database: PDB / ID: 6l4x
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
Asparaginyl endopeptidase
Similarity search - Component
Biological speciesClitoria ternatea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.644 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_peptide_omega / pdbx_validate_rmsd_angle / 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.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 6, 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: Asparaginyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)55,7881
Polymers55,7881
Non-polymers00
Water3,621201
1
A: Asparaginyl endopeptidase

A: Asparaginyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)111,5762
Polymers111,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area2240 Å2
ΔGint-16 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.900, 79.290, 134.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Asparaginyl endopeptidase / Butelase 2


Mass: 55787.902 Da / Num. of mol.: 1 / Mutation: G182A,P183A,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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 42.82 %
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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.64→79.09 Å / Num. obs: 14697 / % possible obs: 100 % / Redundancy: 6 % / Net I/σ(I): 6.4
Reflection shellResolution: 2.64→2.79 Å / Mean I/σ(I) obs: 2.7

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Processing

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

6l4v


Resolution: 2.644→51 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.87 / SU R Cruickshank DPI: 1.033 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.308 / SU Rfree Cruickshank DPI: 0.3
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 709 -RANDOM
Rwork0.207 ---
obs0.2084 14697 100 %-
Displacement parametersBiso mean: 27.65 Å2
Baniso -1Baniso -2Baniso -3
1--7.8596 Å20 Å20 Å2
2--4.2764 Å20 Å2
3---3.5832 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.644→51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 2292 201 3435
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083309HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014474HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1135SINUSOIDAL2
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_it3309HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion19.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion413SEMIHARMONIC5
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_contact2629SEMIHARMONIC4
LS refinement shellResolution: 2.64→2.79 Å
RfactorNum. reflection% reflection
Rfree0.2809 18 -
Rwork0.2455 --
obs--100 %

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