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- PDB-4tjx: Crystal structure of protease-associated domain of Arabidopsis VS... -

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Basic information

Entry
Database: PDB / ID: 4tjx
TitleCrystal structure of protease-associated domain of Arabidopsis VSR1 in complex with aleurain peptide
Components
  • Aleurain peptide
  • Vacuolar-sorting receptor 1
KeywordsPROTEIN TRANSPORT / Complex structure / ligand-binding domain / aleurain pepetide / Beta-barrel
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
Vacuolar-sorting receptor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Hordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.902 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 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar-sorting receptor 1
B: Aleurain peptide


Theoretical massNumber of molelcules
Total (without water)18,9012
Polymers18,9012
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-1 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.513, 58.562, 36.583
Angle α, β, γ (deg.)90.00, 90.65, 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: Protein/peptide Aleurain peptide


Mass: 1070.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hordeum vulgare (barley)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.0, 25% PEG 6000

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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: Dec 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→36.58 Å / Num. obs: 10308 / % possible obs: 94.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 21.5
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 7.6 / % possible all: 85.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TJV

4tjv


Resolution: 1.902→36.58 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 1013 9.91 %
Rwork0.1544 --
obs0.1591 10221 94.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 0 160 1339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061203
X-RAY DIFFRACTIONf_angle_d1.041632
X-RAY DIFFRACTIONf_dihedral_angle_d10.375438
X-RAY DIFFRACTIONf_chiral_restr0.066189
X-RAY DIFFRACTIONf_plane_restr0.004208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.902-2.00180.24371310.16271196X-RAY DIFFRACTION88
2.0018-2.12720.23041440.14851290X-RAY DIFFRACTION92
2.1272-2.29140.20651350.14961295X-RAY DIFFRACTION93
2.2914-2.5220.21051460.15411305X-RAY DIFFRACTION94
2.522-2.88680.2071510.15641351X-RAY DIFFRACTION96
2.8868-3.63650.20971530.14511370X-RAY DIFFRACTION97
3.6365-36.58740.17031530.16181401X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.7622 Å / Origin y: 32.3256 Å / Origin z: 9.9638 Å
111213212223313233
T0.0977 Å2-0.0062 Å2-0.0291 Å2-0.1111 Å20.0068 Å2--0.0382 Å2
L0.6136 °2-0.0722 °2-0.1864 °2-0.5311 °20.4573 °2--0.9104 °2
S0.0201 Å °-0.0236 Å °-0.0105 Å °-0.0004 Å °-0.0235 Å °0.0126 Å °0.0462 Å °-0.0229 Å °-0.0016 Å °
Refinement TLS groupSelection details: all

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