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- PDB-5i8f: Crystal structure of St. John's wort Hyp-1 protein in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5i8f
TitleCrystal structure of St. John's wort Hyp-1 protein in complex with melatonin
ComponentsPhenolic oxidative coupling protein
KeywordsPLANT PROTEIN / PLANT HORMONE BINDING / PHYTOHORMONE BINDING / MELATONIN / CYTOKININ / PLANT DEFENSE / PATHOGENESIS-RELATED PROTEIN / PR-10 PROTEIN / HYPERICIN / DEPRESSION / PR-10 FOLD / HYDROPHOBIC CAVITY / ANS DISPLACEMENT ASSAY (ADA)
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide / Unknown ligand / Phenolic oxidative coupling protein
Similarity search - Component
Biological speciesHypericum perforatum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSliwiak, J. / Dauter, Z. / Jaskolski, M.
Funding support United States, Poland, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
National Science Centre2013/10/M/NZ1/00251 Poland
Citation
Journal: Front Plant Sci / Year: 2016
Title: Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin.
Authors: Sliwiak, J. / Dauter, Z. / Jaskolski, M.
#1: Journal: J.Struct.Biol. / Year: 2010
Title: Crystal Structure Of Hyp-1, A St. John'S Wort Protein Implicated In The Biosynthesis Of Hypericin.
Authors: Michalska, K. / Fernandes, H. / Sikorski, M. / Jaskolski, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Ans Complex Of St John'S Wort Pr-10 Protein With 28 Copies In The Asymmetric Unit: A Fiendish Combination Of Pseudosymmetry With Tetartohedral Twinning.
Authors: Sliwiak, J. / Dauter, Z. / Kowiel, M. / Mccoy, A.J. / Read, R.J. / Jaskolski, M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Likelihood-Based Molecular-Replacement Solution For A Highly Pathological Crystal With Tetartohedral Twinning And Sevenfold Translational Noncrystallographic Symmetry.
Authors: Sliwiak, J. / Jaskolski, M. / Dauter, Z. / Mccoy, A.J. / Read, R.J.
#4: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal Structures Of Two Homologous Pathogenesis-Related Proteins From Yellow Lupine.
Authors: Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#5: Journal: J.Mol.Biol. / Year: 2008
Title: Lupinus Luteus Pathogenesis-Related Protein As A Reservoir For Cytokinin.
Authors: Fernandes, H. / Pasternak, O. / Bujacz, G. / Bujacz, A. / Sikorski, M.M. / Jaskolski, M.
#6: Journal: Febs J. / Year: 2009
Title: Cytokinin-Induced Structural Adaptability Of A Lupinus Luteus Pr-10 Protein.
Authors: Fernandes, H. / Bujacz, A. / Bujacz, G. / Jelen, F. / Jasinski, M. / Kachlicki, P. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#7: Journal: Plant Cell / Year: 2006
Title: Crystal Structure Of Vigna Radiata Cytokinin-Specific Binding Protein In Complex With Zeatin.
Authors: Pasternak, O. / Bujacz, G.D. / Fujimoto, Y. / Hashimoto, Y. / Jelen, F. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#8: Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The Landscape Of Cytokinin Binding By A Plant Nodulin.
Authors: Ruszkowski, M. / Szpotkowski, K. / Sikorski, M. / Jaskolski, M.
#9: Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Specific Binding Of Gibberellic Acid By Cytokinin-Specific Binding Proteins: A New Aspect Of Plant Hormone-Binding Proteins With The Pr-10 Fold.
Authors: Ruszkowski, M. / Sliwiak, J. / Ciesielska, A. / Barciszewski, J. / Sikorski, M. / Jaskolski, M.
#10: Journal: J.Struct.Biol. / Year: 2016
Title: Crystallographic And Cd Probing Of Ligand-Induced Conformational Changes In A Plant Pr-10 Protein.
Authors: Sliwiak, J. / Dolot, R. / Michalska, K. / Szpotkowski, K. / Bujacz, G. / Sikorski, M. / Jaskolski, M.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.3Jan 23, 2019Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id
Revision 1.5Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,21314
Polymers18,4951
Non-polymers71813
Water3,621201
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-32 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.860, 89.639, 76.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phenolic oxidative coupling protein


Mass: 18495.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypericum perforatum (plant) / Gene: hyp1 / Plasmid: PET151/D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9JSA3*PLUS

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Non-polymers , 5 types, 214 molecules

#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 6 / Source method: obtained synthetically
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ML1 / N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide / Melatonin


Mass: 232.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.82 Å3/Da / Density % sol: 56.4 % / Description: prismatic
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1 M citrate (pH 6.5), 20% glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 51868 / % possible obs: 99.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.057 / Net I/av σ(I): 28.9 / Net I/σ(I): 17
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameClassification
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ie5

3ie5


Resolution: 1.3→30 Å / Cross valid method: FREE R-VALUE
Details: Anisotropic refinement. H atoms were added at riding positions.
RfactorNum. reflection% reflection
Rfree0.153 2630 5.1 %
Rwork0.128 --
obs-51868 99.9 %
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 55 201 1551
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond lenghts0.017
X-RAY DIFFRACTIONangles1.6

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