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- PDB-5nij: Crystal structure of arabidopsis thaliana legumain isoform gamma ... -

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Basic information

Entry
Database: PDB / ID: 5nij
TitleCrystal structure of arabidopsis thaliana legumain isoform gamma in two-chain activation state
ComponentsVacuolar-processing enzyme gamma-isozyme
KeywordsLIGASE / Asparaginyl endopeptidase / Vacuolar processing enzyme / Cysteine protease
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
CITRIC ACID / Vacuolar-processing enzyme gamma-isozyme
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsZauner, F.B. / Dall, E. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW_01213 Austria
CitationJournal: Plant Cell / Year: 2018
Title: Crystal Structure of Plant Legumain Reveals a Unique Two-Chain State with pH-Dependent Activity Regulation.
Authors: Zauner, F.B. / Dall, E. / Regl, C. / Grassi, L. / Huber, C.G. / Cabrele, C. / Brandstetter, H.
History
DepositionMar 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 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

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Assembly

Deposited unit
A: Vacuolar-processing enzyme gamma-isozyme
B: Vacuolar-processing enzyme gamma-isozyme
C: Vacuolar-processing enzyme gamma-isozyme
D: Vacuolar-processing enzyme gamma-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,81410
Polymers202,1414
Non-polymers6726
Water1,42379
1
A: Vacuolar-processing enzyme gamma-isozyme
B: Vacuolar-processing enzyme gamma-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5516
Polymers101,0712
Non-polymers4804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Vacuolar-processing enzyme gamma-isozyme
D: Vacuolar-processing enzyme gamma-isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2634
Polymers101,0712
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.830, 147.830, 101.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 50535.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g32940, F26P21.60 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q39119, legumain
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 and 1.6 M MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.75→72.86 Å / Num. obs: 56996 / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.6
Reflection shellResolution: 2.75→2.83 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4411 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FGU

4fgu


Resolution: 2.75→66.112 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 2707 4.75 %
Rwork0.2137 --
obs0.2155 56952 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→66.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13357 0 38 79 13474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313736
X-RAY DIFFRACTIONf_angle_d0.71418589
X-RAY DIFFRACTIONf_dihedral_angle_d12.2644986
X-RAY DIFFRACTIONf_chiral_restr0.0431955
X-RAY DIFFRACTIONf_plane_restr0.0052452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.80.34551410.30982855X-RAY DIFFRACTION100
2.8-2.85390.35331440.31362821X-RAY DIFFRACTION100
2.8539-2.91210.36141400.30942831X-RAY DIFFRACTION100
2.9121-2.97540.33541420.29852845X-RAY DIFFRACTION100
2.9754-3.04470.31461460.28422825X-RAY DIFFRACTION100
3.0447-3.12080.31521180.28172880X-RAY DIFFRACTION100
3.1208-3.20520.31461520.27132836X-RAY DIFFRACTION100
3.2052-3.29950.28551470.25562824X-RAY DIFFRACTION100
3.2995-3.4060.29731420.25652857X-RAY DIFFRACTION100
3.406-3.52770.27071640.24122842X-RAY DIFFRACTION100
3.5277-3.66890.27721550.2322824X-RAY DIFFRACTION100
3.6689-3.83590.25881430.212834X-RAY DIFFRACTION100
3.8359-4.03810.23911470.19142861X-RAY DIFFRACTION100
4.0381-4.29110.23531280.19062876X-RAY DIFFRACTION100
4.2911-4.62230.21111120.18192902X-RAY DIFFRACTION100
4.6223-5.08730.21671590.17492845X-RAY DIFFRACTION100
5.0873-5.82310.23251530.17992839X-RAY DIFFRACTION99
5.8231-7.33490.22991350.19952889X-RAY DIFFRACTION100
7.3349-66.13070.18371390.16292959X-RAY DIFFRACTION100

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