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Yorodumi- PDB-3iv7: Crystal structure of Iron-containing alcohol dehydrogenase (NP_60... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iv7 | ||||||
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Title | Crystal structure of Iron-containing alcohol dehydrogenase (NP_602249.1) from Corynebacterium glutamicum ATCC 13032 KITASATO at 2.07 A resolution | ||||||
Components | Alcohol dehydrogenase IV | ||||||
Keywords | OXIDOREDUCTASE / NP_602249.1 / Iron-containing alcohol dehydrogenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information maleylacetate reductase / maleylacetate reductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Iron-containing alcohol dehydrogenase (NP_602249.1) from Corynebacterium glutamicum ATCC 13032 KITASATO at 2.07 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iv7.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iv7.ent.gz | 118.8 KB | Display | PDB format |
PDBx/mmJSON format | 3iv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/3iv7 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/3iv7 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION |
-Components
#1: Protein | Mass: 38769.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg3386, Cgl3057, NP_602249.1, tcbF / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8NL91, maleylacetate reductase #2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT (RESIDUES 1-363) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 1-363) WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.0000M LiCl, 20.0000% PEG-6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97775 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 2009 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97775 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.07→28.88 Å / Num. obs: 45653 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.586 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 14.29 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.07→28.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 9.225 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.17 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION SOLUTION AND ETHYLENE GLYCOL (EDO) USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. 5).ELECTRON DENSITY NEAR GLY 97 AND GLY 98 ON THE A SUBUNIT WAS NOT MODELED. THIS EXTRA ELECTRON DENSITY IS BELIEVED TO BE ATTRIBUTED TO A PARTIALLY OCCUPIED NICOTINAMIDE-ADENINE- DINUCLEOTIDE (NAD) COFACTOR MOLECULE. THIS TENTATIVE ASSIGNMENT IS BASED ON THE BINDING OF THE COFACTOR AT THE SAME RELATIVE LOCATION IN A SIMILAR STRUCTURE, MALEYLACETATE REDUCTASE FROM AGROBACTERIUM TUMEFACIENS, PDB ID 3HL0.
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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 max: 70.45 Å2 / Biso mean: 30.569 Å2 / Biso min: 15.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→28.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4280 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.07→2.124 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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