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Yorodumi- PDB-6c76: Structure of Iron containing alcohol dehydrogenase from Thermococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c76 | ||||||
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Title | Structure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in an orthorhombic crystal form | ||||||
Components | Alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Alcohol dehydrogenase / Iron-containing / OGL-20P | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermococcus thioreducens (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Larson, S.B. / McPherson, A. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2019 Title: The structure of an iron-containing alcohol dehydrogenase from a hyperthermophilic archaeon in two chemical states. Authors: Larson, S.B. / Jones, J.A. / McPherson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c76.cif.gz | 591.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c76.ent.gz | 496.2 KB | Display | PDB format |
PDBx/mmJSON format | 6c76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c76_validation.pdf.gz | 797.9 KB | Display | wwPDB validaton report |
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Full document | 6c76_full_validation.pdf.gz | 805.8 KB | Display | |
Data in XML | 6c76_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 6c76_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/6c76 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/6c76 | HTTPS FTP |
-Related structure data
Related structure data | 6c75SC 6c7lC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41569.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus thioreducens (archaea) / Gene: AMR53_06445, SAMN05216170_0411 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q2QQL1 |
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-Non-polymers , 5 types, 297 molecules
#2: Chemical | ChemComp-FE / |
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#3: Chemical | ChemComp-NAP / |
#4: Chemical | ChemComp-ACY / |
#5: Chemical | ChemComp-PGE / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate, 10% PEG 10,000 at pH 4.6 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 18, 2013 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.97 Å / Num. obs: 41831 / % possible obs: 90 % / Redundancy: 20.4 % / Biso Wilson estimate: 36.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.041 / Rrim(I) all: 0.214 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1309 / CC1/2: 0.222 / Rpim(I) all: 0.67 / Rrim(I) all: 1.192 / % possible all: 35.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6C75 Resolution: 2.1→33.04 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.945 / SU B: 13.459 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.181 / Stereochemistry target values: Maximum Likelihood Details: HYDROGENS WERE GENERATED BY REFMAC AND ALLOWED TO RIDE ON THE ATOMS TO WHICH THEY WERE ATTACHED UNLESS MOVED TO RELIEVE VAN DER WAALS CONTACTS.
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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: Babinet Model with mask | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.619 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→33.04 Å
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Refine LS restraints |
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