+Open data
-Basic information
Entry | Database: PDB / ID: 7z3s | ||||||
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Title | CRYSTAL STRUCTURE of PheF from Geobacillus stearothermophilus | ||||||
Components | Acetaldehyde dehydrogenase | ||||||
Keywords | LYASE / LYASE-OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / : / NAD binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Driller, R. / Haack, M. / Brueck, T. / Loll, B. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: CRYSTAL STRUCTURE OF THE P1 trifluoroethylglycine (TfeGly) BPTI MUTANT- BOVINE CHYMOTRYPSIN COMPLEX Authors: Leppkes, J. / Wehrhan, L. / Dimos, N. / Loll, B. / Hohmann, T. / Dyrks, M. / Wieseke, A. / Wahl, M.C. / Keller, B.G. / Koksch, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z3s.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z3s.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 7z3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/7z3s ftp://data.pdbj.org/pub/pdb/validation_reports/z3/7z3s | HTTPS FTP |
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-Related structure data
Related structure data | 1nvmS S: Starting model for refinement |
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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: 31870.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: pheF / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B0VXM6, acetaldehyde dehydrogenase (acetylating) | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 M di-Ammonium hydrogen phosphate 15% PEG3350 / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→35 Å / Num. obs: 28151 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 43.54 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.086 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.99→2.11 Å / Redundancy: 13.1 % / Num. unique obs: 4169 / CC1/2: 0.57 / Rrim(I) all: 1.539 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NVM Resolution: 1.99→34.62 Å / SU ML: 0.2486 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 23.5486 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→34.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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