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- PDB-6sjj: A new modulated crystal structure of ANS complex of St John's wor... -

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Basic information

Entry
Database: PDB / ID: 6sjj
TitleA new modulated crystal structure of ANS complex of St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell
ComponentsPR-10 protein
KeywordsPLANT PROTEIN / PLANT HORMONE BINDING / PHYTOHORMONE BINDING / CYTOKININ / PLANT DEFENSE / PATHOGENESIS-RELATED PROTEIN / PR-10 PROTEIN / HYPERICIN / DEPRESSION / PR-10 FOLD / HYDROPHOBIC CAVITY / GLYCINE-RICH LOOP / ANS DISPLACEMENT ASSAY (ADA) / COMMENSURATELY MODULATED SUPERSTRUCTURE / TETARTOHEDRAL TWINNING
Function / homology
Function and homology information


response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
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
8-ANILINO-1-NAPHTHALENE SULFONATE / CITRATE ANION / PR-10 protein
Similarity search - Component
Biological speciesHypericum perforatum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSmietanska, J. / Sliwiak, J. / Gilski, M. / Dauter, Z. / Strzalka, R. / Wolny, J. / Jaskolski, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: A new modulated crystal structure of the ANS complex of the St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell.
Authors: Smietanska, J. / Sliwiak, J. / Gilski, M. / Dauter, Z. / Strzalka, R. / Wolny, J. / Jaskolski, M.
History
DepositionAug 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: PR-10 protein
A: PR-10 protein
R: PR-10 protein
Q: PR-10 protein
P: PR-10 protein
O: PR-10 protein
N: PR-10 protein
M: PR-10 protein
L: PR-10 protein
K: PR-10 protein
J: PR-10 protein
I: PR-10 protein
H: PR-10 protein
G: PR-10 protein
F: PR-10 protein
E: PR-10 protein
D: PR-10 protein
C: PR-10 protein
f: PR-10 protein
e: PR-10 protein
d: PR-10 protein
c: PR-10 protein
b: PR-10 protein
a: PR-10 protein
Z: PR-10 protein
Y: PR-10 protein
X: PR-10 protein
W: PR-10 protein
V: PR-10 protein
U: PR-10 protein
T: PR-10 protein
S: PR-10 protein
j: PR-10 protein
i: PR-10 protein
h: PR-10 protein
g: PR-10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)709,450214
Polymers659,69636
Non-polymers49,754178
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area122800 Å2
ΔGint9 kcal/mol
Surface area271170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.850, 145.850, 385.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 36 molecules BARQPONMLKJIHGFEDCfedcbaZYXWVU...

#1: Protein ...
PR-10 protein


Mass: 18324.898 Da / Num. of mol.: 36 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypericum perforatum (plant) / Gene: PR10.1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160HRF0

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Non-polymers , 6 types, 330 molecules

#2: Chemical...
ChemComp-2AN / 8-ANILINO-1-NAPHTHALENE SULFONATE / 8-Anilinonaphthalene-1-sulfonic acid


Mass: 299.344 Da / Num. of mol.: 157 / Source method: obtained synthetically / Formula: C16H13NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES buffer pH 7.5, 1.3 M sodium citrate precipitant pH 6.3, 1:1 protein:reservoir volume ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 12, 2014
RadiationMonochromator: SI(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.241
11K, H, -L20.242
11-K, -H, -L30.233
11h,-k,-l40.284
ReflectionResolution: 2.3→31.58 Å / Num. obs: 127324 / % possible obs: 99.28 % / Redundancy: 7.2 % / Biso Wilson estimate: 67.46 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.066 / Net I/σ(I): 6.22
Reflection shellResolution: 2.3→2.39 Å / Rmerge(I) obs: 0.691 / Num. unique obs: 24778 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N3E

4n3e


Resolution: 2.3→31.58 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.176 / SU ML: 0.188 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.047 / Details: Hydrogen atoms were added at riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 3974 1.1 %RANDOM
Rwork0.226 ---
obs0.2264 123350 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 322.63 Å2 / Biso mean: 67.461 Å2 / Biso min: 16.02 Å2
Baniso -1Baniso -2Baniso -3
1--26.22 Å2-0 Å2-10.81 Å2
2--6.51 Å20 Å2
3---19.72 Å2
Refinement stepCycle: final / Resolution: 2.3→31.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44726 0 3465 152 48343
Biso mean--67.44 46.63 -
Num. residues----5777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01549551
X-RAY DIFFRACTIONr_bond_other_d0.0030.01743786
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.76767452
X-RAY DIFFRACTIONr_angle_other_deg1.0861.693101409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.54255741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.324.0782082
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.806157547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.52515102
X-RAY DIFFRACTIONr_chiral_restr0.0830.26113
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0254912
X-RAY DIFFRACTIONr_gen_planes_other0.0140.0210938
LS refinement shellResolution: 2.301→2.356 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rwork0.18 24778 -
obs--94.2 %

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