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- PDB-3ccg: Crystal structure of predicted HD superfamily hydrolase involved ... -
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Basic information
Entry | Database: PDB / ID: 3ccg | ||||||
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Title | Crystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution | ||||||
![]() | HD superfamily hydrolase | ||||||
![]() | HYDROLASE / NP_347894.1 / predicted HD superfamily hydrolase involved in NAD metabolism / HD domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.4 KB | Display | ![]() |
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PDB format | ![]() | 43 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 429.1 KB | Display | ![]() |
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Full document | ![]() | 430.3 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21759.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Clostridium acetobutylicum / Strain: DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 / Gene: NP_347894.1, CA_C1263 / Plasmid: SpeedET / Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. THE TAG WAS REMOVED WITH TEV ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: NANODROP, 0.2M Mg formate, 20.0% PEG 3350, 0.001M Spermine tetra-HCl, No Buffer pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 1, 2008 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→25.872 Å / Num. obs: 30979 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.062 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.53 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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. IRON HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE BASED ON AN X-RAY FLUORESCENCE SCAN FOR METAL, ANOMALOUS DIFFERENCE FOURIERS, AND COORDINATION GEOMETRY. 5. PHOSPHATE IS MODELED BASED ON ELECTRON DENSITY AND PROPOSED FUNCTION.
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.356 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→25.872 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å
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