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- PDB-6xt5: Jack bean asparaginyl endopeptidase -

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Basic information

Entry
Database: PDB / ID: 6xt5
TitleJack bean asparaginyl endopeptidase
ComponentsLegumain
KeywordsPLANT PROTEIN / Hydrolase / Asparaginyl endopeptidase
Function / homologyLegumain beta / legumain / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity / Legumain
Function and homology information
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsNonis, S.G. / Haywood, J. / Schmidberger, J.W. / Bond, C.S.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160100107 Australia
Australian Research Council (ARC)DE180101445 Australia
Citation
Journal: Plant Cell / Year: 2021
Title: Structural and biochemical analyses of concanavalin A circular permutation by jack bean asparaginyl endopeptidase.
Authors: Nonis, S.G. / Haywood, J. / Schmidberger, J.W. / Mackie, E.R.R. / Soares da Costa, T.P. / Bond, C.S. / Mylne, J.S.
#1: Journal: Biorxiv / Year: 2020
Title: Structural basis for a natural circular permutation in proteins
Authors: Nonis, S.G. / Haywood, J. / Schmidberger, J.W. / Bond, C.S. / Mylne, J.S.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 29, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Legumain
B: Legumain


Theoretical massNumber of molelcules
Total (without water)100,1282
Polymers100,1282
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-15 kcal/mol
Surface area33080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.989, 88.882, 109.848
Angle α, β, γ (deg.)90.000, 111.722, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Legumain / Asparaginyl endopeptidase


Mass: 50064.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle Express / References: UniProt: P49046, legumain
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG 20,000, EDTA disodium salt dihydrate / PH range: 7.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.69→46.33 Å / Num. obs: 26353 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.997 / Net I/σ(I): 9.6
Reflection shellResolution: 2.69→2.82 Å / Num. unique obs: 3311 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.16-3549-000refinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NIJ

5nij


Resolution: 2.69→45.611 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.183 / SU B: 19.622 / SU ML: 0.37 / Average fsc free: 0.8219 / Average fsc work: 0.8491 / Cross valid method: FREE R-VALUE / ESU R Free: 0.384
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2683 1323 5.021 %
Rwork0.1958 25028 -
all0.2 --
obs-26351 98.737 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 69.426 Å2
Baniso -1Baniso -2Baniso -3
1--5.007 Å20 Å2-1.323 Å2
2--1.247 Å20 Å2
3---3.654 Å2
Refinement stepCycle: LAST / Resolution: 2.69→45.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6750 0 0 32 6782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136942
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176150
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.6479413
X-RAY DIFFRACTIONr_angle_other_deg1.1261.57514351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9555862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1523.343347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.136151122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7481528
X-RAY DIFFRACTIONr_chiral_restr0.0510.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021412
X-RAY DIFFRACTIONr_nbd_refined0.2030.21693
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.26340
X-RAY DIFFRACTIONr_nbtor_refined0.1630.23329
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23277
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2181
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.210
X-RAY DIFFRACTIONr_nbd_other0.2570.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0810.21
X-RAY DIFFRACTIONr_mcbond_it3.7517.443461
X-RAY DIFFRACTIONr_mcbond_other3.7517.443460
X-RAY DIFFRACTIONr_mcangle_it5.84711.1524318
X-RAY DIFFRACTIONr_mcangle_other5.84611.1534319
X-RAY DIFFRACTIONr_scbond_it3.4437.6923481
X-RAY DIFFRACTIONr_scbond_other3.4437.6933482
X-RAY DIFFRACTIONr_scangle_it5.46611.4465095
X-RAY DIFFRACTIONr_scangle_other5.46511.4465096
X-RAY DIFFRACTIONr_lrange_it8.18787.6887886
X-RAY DIFFRACTIONr_lrange_other8.18687.6937887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.760.505800.3971634X-RAY DIFFRACTION89.1316
2.76-2.8350.408950.361814X-RAY DIFFRACTION99.8953
2.835-2.9170.3041060.3021748X-RAY DIFFRACTION100
2.917-3.0060.33930.31720X-RAY DIFFRACTION99.8898
3.006-3.1040.413700.2811663X-RAY DIFFRACTION99.7697
3.104-3.2130.372770.2451618X-RAY DIFFRACTION99.6473
3.213-3.3330.331810.2331561X-RAY DIFFRACTION99.6964
3.333-3.4690.32750.2291489X-RAY DIFFRACTION99.8085
3.469-3.6220.328580.2151432X-RAY DIFFRACTION99.466
3.622-3.7980.29740.1971378X-RAY DIFFRACTION99.4521
3.798-4.0020.269930.1821287X-RAY DIFFRACTION99.639
4.002-4.2420.221810.1611192X-RAY DIFFRACTION99.6088
4.242-4.5320.197640.1341157X-RAY DIFFRACTION99.2683
4.532-4.8910.187680.1231080X-RAY DIFFRACTION99.308
4.891-5.3520.253520.1431013X-RAY DIFFRACTION99.6258
5.352-5.9740.268480.19889X-RAY DIFFRACTION99.1534
5.974-6.8780.261310.205804X-RAY DIFFRACTION97.2061
6.878-8.3760.289300.175688X-RAY DIFFRACTION98.3562
8.376-11.6510.19220.15539X-RAY DIFFRACTION99.4681
11.651-45.6110.242250.212322X-RAY DIFFRACTION98.5795

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