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- PDB-6ysa: Crystal structure of Arabidopsis thaliana legumain isoform beta i... -

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Basic information

Entry
Database: PDB / ID: 6ysa
TitleCrystal structure of Arabidopsis thaliana legumain isoform beta in zymogen state
ComponentsVacuolar-processing enzyme beta-isozyme
KeywordsHYDROLASE / protease / ligase / proenzyme / vacuolar processing enzyme / VPE
Function / homology
Function and homology information


protein storage vacuole / legumain / vacuolar protein processing / proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity
Similarity search - Function
Legumain beta / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family
Similarity search - Domain/homology
CITRIC ACID / Vacuolar-processing enzyme beta-isozyme
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsDall, E. / Zauner, F.B. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW_01213 Austria
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural and functional studies ofArabidopsis thalianalegumain beta reveal isoform specific mechanisms of activation and substrate recognition.
Authors: Dall, E. / Zauner, F.B. / Soh, W.T. / Demir, F. / Dahms, S.O. / Cabrele, C. / Huesgen, P.F. / Brandstetter, H.
History
DepositionApr 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / 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_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar-processing enzyme beta-isozyme
B: Vacuolar-processing enzyme beta-isozyme
C: Vacuolar-processing enzyme beta-isozyme
D: Vacuolar-processing enzyme beta-isozyme
E: Vacuolar-processing enzyme beta-isozyme
F: Vacuolar-processing enzyme beta-isozyme
G: Vacuolar-processing enzyme beta-isozyme
H: Vacuolar-processing enzyme beta-isozyme
I: Vacuolar-processing enzyme beta-isozyme
J: Vacuolar-processing enzyme beta-isozyme
K: Vacuolar-processing enzyme beta-isozyme
L: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)618,54791
Polymers606,92212
Non-polymers11,62579
Water40,5702252
1
A: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4827
Polymers50,5771
Non-polymers9056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5788
Polymers50,5771
Non-polymers1,0017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5788
Polymers50,5771
Non-polymers1,0017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3856
Polymers50,5771
Non-polymers8095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6748
Polymers50,5771
Non-polymers1,0977
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6749
Polymers50,5771
Non-polymers1,0978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3856
Polymers50,5771
Non-polymers8095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6749
Polymers50,5771
Non-polymers1,0978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,77010
Polymers50,5771
Non-polymers1,1939
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4827
Polymers50,5771
Non-polymers9056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4827
Polymers50,5771
Non-polymers9056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Vacuolar-processing enzyme beta-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3856
Polymers50,5771
Non-polymers8095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.465, 170.465, 196.515
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein
Vacuolar-processing enzyme beta-isozyme / Asparaginyl endopeptidase beta-VPE / Beta-VPE


Mass: 50576.793 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: bVPE, At1g62710, F23N19.7 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q39044, legumain
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 66 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2252 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.5 M ammonium sulfate, 1 M Lithium sulfate and 0.1 M trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.949998 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.949998 Å / Relative weight: 1
ReflectionResolution: 2.01→49.69 Å / Num. obs: 337197 / % possible obs: 90.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 31.21 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.08 / Net I/σ(I): 6.8
Reflection shellResolution: 2.01→2.04 Å / Rmerge(I) obs: 1.4 / Num. unique obs: 15861 / CC1/2: 0.22 / Rpim(I) all: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nij

5nij


Resolution: 2.01→49.68 Å / SU ML: 0.2897 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.5142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2186 17034 5.06 %
Rwork0.2086 319560 -
obs0.2091 336594 90.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 2.01→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39208 0 679 2254 42141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00640719
X-RAY DIFFRACTIONf_angle_d1.148355226
X-RAY DIFFRACTIONf_chiral_restr0.57416051
X-RAY DIFFRACTIONf_plane_restr0.00417060
X-RAY DIFFRACTIONf_dihedral_angle_d14.513514774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.36855560.35679514X-RAY DIFFRACTION81.24
2.03-2.050.34715930.339910830X-RAY DIFFRACTION92.17
2.05-2.080.34746230.33610848X-RAY DIFFRACTION92.37
2.08-2.10.36856020.333910891X-RAY DIFFRACTION92.37
2.1-2.130.34745730.327810888X-RAY DIFFRACTION92.02
2.13-2.160.31916060.30910820X-RAY DIFFRACTION92.41
2.16-2.190.30715830.300210907X-RAY DIFFRACTION92.28
2.19-2.220.3156010.296810832X-RAY DIFFRACTION91.76
2.22-2.260.32595300.284110548X-RAY DIFFRACTION89.55
2.26-2.30.27585600.271610875X-RAY DIFFRACTION91.85
2.3-2.340.30425810.267211013X-RAY DIFFRACTION93.26
2.34-2.380.28145570.262711060X-RAY DIFFRACTION93.58
2.38-2.420.29196240.255210978X-RAY DIFFRACTION93.32
2.42-2.470.27235430.248711038X-RAY DIFFRACTION92.9
2.47-2.530.286340.242310838X-RAY DIFFRACTION92.43
2.53-2.590.26246550.228210700X-RAY DIFFRACTION91.04
2.59-2.650.24845210.226310725X-RAY DIFFRACTION90.66
2.65-2.720.23845620.225210667X-RAY DIFFRACTION90.19
2.72-2.80.23255650.22910479X-RAY DIFFRACTION88.51
2.8-2.890.24735600.227810890X-RAY DIFFRACTION92.03
2.89-30.22825610.224610818X-RAY DIFFRACTION91.54
3-3.120.2175230.216210776X-RAY DIFFRACTION90.73
3.12-3.260.21915240.204110694X-RAY DIFFRACTION89.88
3.26-3.430.21015260.1910425X-RAY DIFFRACTION88.03
3.43-3.640.18045120.16919968X-RAY DIFFRACTION84.01
3.64-3.920.1665560.153310616X-RAY DIFFRACTION89.65
3.92-4.320.13745490.139110577X-RAY DIFFRACTION89.07
4.32-4.940.12385930.130810197X-RAY DIFFRACTION86.28
4.94-6.230.16435100.164410107X-RAY DIFFRACTION84.72
6.23-49.680.18135510.188410041X-RAY DIFFRACTION83.7

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