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- PDB-4tjv: Crystal structure of protease-associated domain of Arabidopsis va... -

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Basic information

Entry
Database: PDB / ID: 4tjv
TitleCrystal structure of protease-associated domain of Arabidopsis vacuolar sorting receptor 1
ComponentsVacuolar-sorting receptor 1
KeywordsPROTEIN TRANSPORT / Ligand-binding domain / Beta barrel / Apo form
Function / homology
Function and homology information


amino-terminal vacuolar sorting propeptide binding / Golgi to vacuole transport / clathrin-coated vesicle membrane / vacuolar transport / protein targeting to vacuole / trans-Golgi network / late endosome / Golgi membrane / calcium ion binding / Golgi apparatus ...amino-terminal vacuolar sorting propeptide binding / Golgi to vacuole transport / clathrin-coated vesicle membrane / vacuolar transport / protein targeting to vacuole / trans-Golgi network / late endosome / Golgi membrane / calcium ion binding / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Glucose Oxidase; domain 1 / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain ...Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Glucose Oxidase; domain 1 / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / EGF-like domain signature 2. / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Vacuolar-sorting receptor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.651 Å
AuthorsLuo, F. / Fong, Y.H. / Jiang, L.W. / Wong, K.B.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
General Research Fund from the Research Grants Council of Hong Kong SAR476212 Hong Kong
CitationJournal: Plant Cell / Year: 2014
Title: How vacuolar sorting receptor proteins interact with their cargo proteins: crystal structures of apo and cargo-bound forms of the protease-associated domain from an Arabidopsis vacuolar sorting receptor.
Authors: Luo, F. / Fong, Y.H. / Zeng, Y. / Shen, J. / Jiang, L. / Wong, K.B.
History
DepositionMay 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar-sorting receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5937
Polymers17,8311
Non-polymers7616
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-2 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.600, 62.680, 35.810
Angle α, β, γ (deg.)90.00, 109.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vacuolar-sorting receptor 1 / AtVSR1 / BP80-like protein b / AtBP80b / Epidermal growth factor receptor-like protein 1 / AtELP1 / ...AtVSR1 / BP80-like protein b / AtBP80b / Epidermal growth factor receptor-like protein 1 / AtELP1 / Spot 3 protein


Mass: 17831.242 Da / Num. of mol.: 1 / Fragment: UNP residues 20-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VSR1, BP80B, ELP, ELP1, At3g52850, F8J2.20 / Production host: Escherichia coli (E. coli) / References: UniProt: P93026
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.94 Å3/Da / Density % sol: 36.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 10% glycerol, 0.1 M MES pH 6.0, 30% PEG 600, 5% (w/v) PEG 1000.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→33.78 Å / Num. obs: 15984 / % possible obs: 97.7 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 74
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 19.1 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.651→33.78 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.84 / Phase error: 18.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1902 798 5.01 %
Rwork0.1662 --
obs0.1675 15966 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.651→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 6 137 1385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071285
X-RAY DIFFRACTIONf_angle_d1.3521752
X-RAY DIFFRACTIONf_dihedral_angle_d11.56470
X-RAY DIFFRACTIONf_chiral_restr0.061202
X-RAY DIFFRACTIONf_plane_restr0.008227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6512-1.70450.24791300.1982645X-RAY DIFFRACTION95
1.7045-1.76540.2271530.18092630X-RAY DIFFRACTION96
1.7654-1.8360.20221350.17422648X-RAY DIFFRACTION96
1.836-1.91960.24411570.16382683X-RAY DIFFRACTION97
1.9196-2.02080.2081460.15592701X-RAY DIFFRACTION97
2.0208-2.14740.17341550.15532711X-RAY DIFFRACTION98
2.1474-2.31310.18421250.1632742X-RAY DIFFRACTION98
2.3131-2.54590.21481180.1732758X-RAY DIFFRACTION99
2.5459-2.91410.19131400.18242739X-RAY DIFFRACTION99
2.9141-3.67070.18631470.16432781X-RAY DIFFRACTION100
3.6707-33.78590.16031640.15642755X-RAY DIFFRACTION100

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