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- PDB-5obt: Fully activated A. thaliana legumain isoform gamma in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5obt
TitleFully activated A. thaliana legumain isoform gamma in complex with Ac-YVAD-CMK
Components
  • (Vacuolar-processing enzyme gamma-isozyme) x 2
  • Ac-YVAD-CMK
KeywordsHYDROLASE / Legumain / Asparaginyl endopeptidase / Vacuolar processing enzyme / peptide cyclase
Function / homology
Function and homology information


lytic vacuole / protein storage vacuole / legumain / response to ethylene / response to salicylic acid / leaf senescence / vacuolar protein processing / response to jasmonic acid / proteolysis involved in protein catabolic process / response to wounding ...lytic vacuole / protein storage vacuole / legumain / response to ethylene / response to salicylic acid / leaf senescence / vacuolar protein processing / response to jasmonic acid / proteolysis involved in protein catabolic process / response to wounding / endopeptidase activity / cysteine-type endopeptidase activity
Similarity search - Function
Asparaginyl endopeptidase / Legumain prodomain superfamily / : / Legumain, prodomain / Peptidase C13, legumain / Peptidase C13 family / Rossmann fold - #1460 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACE-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE / Vacuolar-processing enzyme gamma-isozyme
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZauner, B.F. / Dall, E. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW_01213 Austria
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural analyses ofArabidopsis thalianalegumain gamma reveal differential recognition and processing of proteolysis and ligation substrates.
Authors: Zauner, F.B. / Elsasser, B. / Dall, E. / Cabrele, C. / Brandstetter, H.
History
DepositionJun 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 13, 2018Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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_rmsd_angle / 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 / _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 2.1Jan 17, 2024Group: 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: Vacuolar-processing enzyme gamma-isozyme
E: Vacuolar-processing enzyme gamma-isozyme
C: Ac-YVAD-CMK
B: Vacuolar-processing enzyme gamma-isozyme
F: Vacuolar-processing enzyme gamma-isozyme
D: Ac-YVAD-CMK


Theoretical massNumber of molelcules
Total (without water)66,5586
Polymers66,5586
Non-polymers00
Water12,070670
1
A: Vacuolar-processing enzyme gamma-isozyme
E: Vacuolar-processing enzyme gamma-isozyme
C: Ac-YVAD-CMK


Theoretical massNumber of molelcules
Total (without water)33,2793
Polymers33,2793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-16 kcal/mol
Surface area12190 Å2
MethodPISA
2
B: Vacuolar-processing enzyme gamma-isozyme
F: Vacuolar-processing enzyme gamma-isozyme
D: Ac-YVAD-CMK


Theoretical massNumber of molelcules
Total (without water)33,2793
Polymers33,2793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-17 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.740, 78.070, 77.719
Angle α, β, γ (deg.)90.00, 92.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vacuolar-processing enzyme gamma-isozyme / Asparaginyl endopeptidase gamma-VPE / Gamma-VPE


Mass: 26987.801 Da / Num. of mol.: 2 / Fragment: Cleaved N-terminus, UNP residues 56-283
Source method: isolated from a genetically manipulated source
Details: Residue D176 is found to be converted to SNN / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g32940, F26P21.60 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q39119, legumain
#2: Protein Vacuolar-processing enzyme gamma-isozyme / Asparaginyl endopeptidase gamma-VPE / Gamma-VPE


Mass: 5766.393 Da / Num. of mol.: 2 / Fragment: Cleaved C-terminus, UNP Residues 284-334
Source method: isolated from a genetically manipulated source
Details: Residue D176 is found to be converted to SNN / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g32940, F26P21.60 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q39119, legumain
#3: Protein/peptide Ac-YVAD-CMK


Type: Peptide-like / Class: Inhibitor / Mass: 524.996 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: ACE-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 4% PEG 4000, 100 mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.5→24.56 Å / Num. obs: 74201 / % possible obs: 93.5 % / Redundancy: 2.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Rrim(I) all: 0.07 / Net I/σ(I): 8.3
Reflection shellHighest resolution: 1.5 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7215 / Num. unique obs: 3597 / CC1/2: 0.78 / Rpim(I) all: 0.24 / Rrim(I) all: 0.34 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nij

5nij


Resolution: 1.5→24.558 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1819 3606 4.86 %
Rwork0.1516 --
obs0.1531 74167 93.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→24.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4395 0 2 670 5067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064648
X-RAY DIFFRACTIONf_angle_d1.1346329
X-RAY DIFFRACTIONf_dihedral_angle_d11.8911670
X-RAY DIFFRACTIONf_chiral_restr0.065660
X-RAY DIFFRACTIONf_plane_restr0.005845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51970.26261380.23762571X-RAY DIFFRACTION91
1.5197-1.54060.23081410.21712812X-RAY DIFFRACTION96
1.5406-1.56260.25961320.21262789X-RAY DIFFRACTION96
1.5626-1.58590.2341140.19712803X-RAY DIFFRACTION95
1.5859-1.61070.22781160.18992798X-RAY DIFFRACTION95
1.6107-1.63710.24661220.19082723X-RAY DIFFRACTION94
1.6371-1.66530.24411630.18562697X-RAY DIFFRACTION94
1.6653-1.69560.19051370.18442688X-RAY DIFFRACTION92
1.6956-1.72820.241410.19162566X-RAY DIFFRACTION89
1.7282-1.76340.20631580.17862753X-RAY DIFFRACTION95
1.7634-1.80180.21111480.16832762X-RAY DIFFRACTION95
1.8018-1.84370.19061680.15932774X-RAY DIFFRACTION96
1.8437-1.88970.1981630.15562741X-RAY DIFFRACTION95
1.8897-1.94080.17751420.14942706X-RAY DIFFRACTION94
1.9408-1.99790.1921090.14852767X-RAY DIFFRACTION93
1.9979-2.06240.19181240.14862588X-RAY DIFFRACTION89
2.0624-2.1360.17371270.14352734X-RAY DIFFRACTION94
2.136-2.22150.15581430.14152781X-RAY DIFFRACTION95
2.2215-2.32250.17661340.1392754X-RAY DIFFRACTION94
2.3225-2.44490.15521170.14792760X-RAY DIFFRACTION94
2.4449-2.59790.17771390.1422662X-RAY DIFFRACTION91
2.5979-2.79820.16151160.14852682X-RAY DIFFRACTION92
2.7982-3.07930.19611570.1472704X-RAY DIFFRACTION93
3.0793-3.52380.16511640.13472650X-RAY DIFFRACTION91
3.5238-4.43540.14111300.1152621X-RAY DIFFRACTION89
4.4354-24.56140.14781630.13412675X-RAY DIFFRACTION90

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