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Yorodumi- PDB-8ozo: Populus tremula stable protein 1 with N-terminal binding peptide ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ozo | ||||||
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Title | Populus tremula stable protein 1 with N-terminal binding peptide extension | ||||||
Components | Stable protein 1 | ||||||
Keywords | PLANT PROTEIN / Hemine / Protein engineering / Biohybrid / catalysis | ||||||
Function / homology | Stress-response A/B barrel domain-containing protein HS1/DABB1-like / Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Dimeric alpha-beta barrel / Stable protein 1 Function and homology information | ||||||
Biological species | Populus tremula (European aspen) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sklyar, J. / Zeibaq, Y. / Bachar, O. / Yehezkeli, O. / Adir, N. | ||||||
Funding support | 1items
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Citation | Journal: Small Science / Year: 2024 Title: A Bioengineered Stable Protein 1-Hemin Complex with Enhanced Peroxidase-Like Catalytic Properties Authors: Sklyar, J. / Zeibaq, Y. / Bachar, O. / Yehezkeli, O. / Adir, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ozo.cif.gz | 547 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ozo.ent.gz | 448.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ozo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ozo_validation.pdf.gz | 613.8 KB | Display | wwPDB validaton report |
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Full document | 8ozo_full_validation.pdf.gz | 632.6 KB | Display | |
Data in XML | 8ozo_validation.xml.gz | 106.6 KB | Display | |
Data in CIF | 8ozo_validation.cif.gz | 150.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/8ozo ftp://data.pdbj.org/pub/pdb/validation_reports/oz/8ozo | HTTPS FTP |
-Related structure data
Related structure data | 8oz4C 8ozsC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13681.366 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus tremula (European aspen) / Gene: sp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AR79 #2: Water | ChemComp-HOH / | |
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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: 2.58 Å3/Da / Density % sol: 47.42 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2M Potassium sodium tartrate tetrahydrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873128 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.16 Å / Num. obs: 118409 / % possible obs: 99.8 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.117 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.4→2.44 Å / Num. unique obs: 5849 / CC1/2: 0.968 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.16 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→48.16 Å
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Refine LS restraints |
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LS refinement shell |
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