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- PDB-6l4v: Turning an asparaginyl endopeptidase into a peptide ligase -

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Basic information

Entry
Database: PDB / ID: 6l4v
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 / : / 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: 1.35 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 / 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 2.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Asparaginyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1907
Polymers55,7741
Non-polymers4166
Water9,656536
1
A: Asparaginyl endopeptidase
hetero molecules

A: Asparaginyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,38114
Polymers111,5482
Non-polymers83312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5110 Å2
ΔGint24 kcal/mol
Surface area31290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 133.800, 44.250
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: 55773.875 Da / Num. of mol.: 1
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 536 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
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 Sodium HEPES; 0.1M MOPS 10% v/v ...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 Sodium HEPES; 0.1M MOPS 10% v/v Ethylene glycol; 8 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 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: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.35→19.75 Å / Num. obs: 103635 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.05729 / Net I/σ(I): 14.16
Reflection shellResolution: 1.35→1.39 Å / Rmerge(I) obs: 1.58 / Mean I/σ(I) obs: 0.9

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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: 5H0I

5h0i


Resolution: 1.35→19.75 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.049 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.053 / SU Rfree Blow DPI: 0.052 / SU Rfree Cruickshank DPI: 0.049
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 5182 -RANDOM
Rwork0.1744 ---
obs0.1751 103619 99.8 %-
Displacement parametersBiso mean: 26.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.3094 Å20 Å20 Å2
2--3.1705 Å20 Å2
3----1.8611 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.35→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 2327 536 3807
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093405HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14604HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1177SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes585HARMONIC5
X-RAY DIFFRACTIONt_it3405HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.65
X-RAY DIFFRACTIONt_other_torsion15.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion419SEMIHARMONIC5
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_contact3923SEMIHARMONIC4
LS refinement shellResolution: 1.35→1.39 Å
RfactorNum. reflection% reflection
Rfree0.3071 104 -
Rwork0.2715 --
obs--96.83 %

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