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Yorodumi- PDB-8oz4: Populus tremula stable protein 1 with an alternate crystal lattice -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oz4 | ||||||
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Title | Populus tremula stable protein 1 with an alternate crystal lattice | ||||||
Components | Stable protein 1 | ||||||
Keywords | PLANT PROTEIN / Protein engineering | ||||||
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: 3.1 Å | ||||||
Authors | Sklyar, J. / Zeibaq, Y. / Bachar, O. / Yehezkeli, O. / Adir, N. | ||||||
Funding support | Israel, 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 | 8oz4.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oz4.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 8oz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oz4_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 8oz4_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 8oz4_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 8oz4_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/8oz4 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/8oz4 | HTTPS FTP |
-Related structure data
Related structure data | 8ozoC 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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Unit cell |
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-Components
#1: Protein | Mass: 12422.962 Da / Num. of mol.: 3 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 |
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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: 2.52 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 0.2N NaCl, 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: ID30B / Wavelength: 0.976253 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976253 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→80.76 Å / Num. obs: 7263 / % possible obs: 99.8 % / Redundancy: 18.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 3.1→3.31 Å / Num. unique obs: 1289 / CC1/2: 0.975 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→44.79 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.92 / 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: 3.1→44.79 Å
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Refine LS restraints |
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LS refinement shell |
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