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Yorodumi- PDB-4n3e: Crystal structure of Hyp-1, a St John's wort PR-10 protein, in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n3e | ||||||
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Title | Crystal structure of Hyp-1, a St John's wort PR-10 protein, in complex with 8-anilino-1-naphthalene sulfonate (ANS) | ||||||
Components | Phenolic oxidative coupling protein | ||||||
Keywords | PLANT 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 | ||||||
Biological species | Hypericum perforatum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Sliwiak, J. / Dauter, Z. / Mccoy, A.J. / Read, R.J. / Jaskolski, M. | ||||||
Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n3e.cif.gz | 895.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n3e.ent.gz | 762.8 KB | Display | PDB format |
PDBx/mmJSON format | 4n3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/4n3e ftp://data.pdbj.org/pub/pdb/validation_reports/n3/4n3e | HTTPS FTP |
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-Related structure data
Related structure data | 3ie5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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28 |
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Unit cell |
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Details | THE PROTEIN IS MONOMERIC IN SOLUTION, BUT FORMS DIMERS IN THE CRYSTAL STRUCTURE VIA ANTIPARALLEL INTERMOLECULAR BETA-SHEETS INVOLVING STRANDS BETA1. THE PAIRING SCHEME IS AB, CD, ..., YZ,... |
-Components
#1: Protein | Mass: 18495.109 Da / Num. of mol.: 28 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypericum perforatum (plant) / Gene: hyp-1, HYP1.1 / Plasmid: pET151/D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8H1L1 #2: Chemical | ChemComp-2AN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | RESIDUES NUMBERED -5 TO 0 ARE FROM A CLONING ARTIFACT. RESIDUES 1-159 ARE FROM THE GENUINE PROTEIN ...RESIDUES NUMBERED -5 TO 0 ARE FROM A CLONING ARTIFACT. RESIDUES 1-159 ARE FROM THE GENUINE PROTEIN SEQUENCE. THE AMINO ACID SEQUENCE OF THE PRESENT PROTEIN DIFFERS FROM THE DEPOSITED SEQUENCE Q8H1L1 POSSIBLY BECAUSE OF GENETIC VARIABILIT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.12 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES 0.1 M, tribasic sodium citrate 1.3 M, glycerol 10% , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2011 / Details: FOCUSING MIRRORS | |||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.43→50 Å / Num. obs: 61810 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 26.435 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2.43→2.52 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2.64 / Num. unique all: 6043 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IE5 Resolution: 2.43→48.87 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: R-FREE / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. The reflection data set for refinement in monoclinic symmetry was obtained by expansion of a tetartohedrally twinned data set merged in tetragonal symmetry
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.042 Å2
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Refinement step | Cycle: LAST / Resolution: 2.43→48.87 Å
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Refine LS restraints |
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