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Yorodumi- PDB-8w08: Crystal Structure of the worst case reconstruction of the ancestr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w08 | |||||||||
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Title | Crystal Structure of the worst case reconstruction of the ancestral triosephosphate isomerase of the last opisthokont common ancestor obtained by maximum likelihood | |||||||||
Components | Triosephosphate isomerase | |||||||||
Keywords | ISOMERASE / Triosephosphate isomerase / ancestral sequence reconstruction | |||||||||
Function / homology | FLUORIDE ION Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | |||||||||
Authors | Perez-Nino, J.A. / Rodriguez-Romero, A. / Guerra-Borrego, Y. / Fernandez-Velasco, D.A. | |||||||||
Funding support | Mexico, 2items
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Citation | Journal: Protein Sci. / Year: 2024 Title: Stable monomers in the ancestral sequence reconstruction of the last opisthokont common ancestor of dimeric triosephosphate isomerase. Authors: Perez-Nino, J.A. / Guerra, Y. / Diaz-Salazar, A.J. / Costas, M. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w08.cif.gz | 214.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w08.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 8w08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8w08_validation.pdf.gz | 432.4 KB | Display | wwPDB validaton report |
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Full document | 8w08_full_validation.pdf.gz | 435.5 KB | Display | |
Data in XML | 8w08_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 8w08_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/8w08 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/8w08 | HTTPS FTP |
-Related structure data
Related structure data | 8v09C 8v0aC 8v2wC 8v2xC 8w05C 8w06C 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: 29384.361 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Ancestral sequence reconstruction of the opisthokont common ancestor Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28T(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: triose-phosphate isomerase #2: Chemical | ChemComp-F / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.43 Å3/Da / Density % sol: 49.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium fluoride, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Feb 4, 2019 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→32.52 Å / Num. obs: 43361 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Χ2: 0.98 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.88→1.92 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2757 / CC1/2: 0.875 / Χ2: 0.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→32.52 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.75 / 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: 1.88→32.52 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.19 Å / Origin y: -19.5015 Å / Origin z: 9.0496 Å
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Refinement TLS group | Selection details: all |