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- PDB-4rgb: Crystal structure of a putative carveol dehydrogenase from Mycoba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rgb | ||||||
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Title | Crystal structure of a putative carveol dehydrogenase from Mycobacterium avium bound to NAD | ||||||
![]() | Carveol dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / putative non-exchangeable NAD | ||||||
Function / homology | ![]() (+)-trans-carveol dehydrogenase / (+)-trans-carveol dehydrogenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors. Authors: Haft, D.H. / Pierce, P.G. / Mayclin, S.J. / Sullivan, A. / Gardberg, A.S. / Abendroth, J. / Begley, D.W. / Phan, I.Q. / Staker, B.L. / Myler, P.J. / Marathias, V.M. / Lorimer, D.D. / Edwards, T.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.4 KB | Display | ![]() |
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PDB format | ![]() | 180.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3oecC ![]() 3pgxC ![]() 3pxxC ![]() 3s55C ![]() 3sx2C ![]() 3t7cC ![]() 3tscSC ![]() 5ej2C C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 16 - 289 / Label seq-ID: 21 - 294
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Components
#1: Protein | Mass: 31626.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0QDP5, UniProt: A0A0H2ZU39*PLUS, (+)-trans-carveol dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.82 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MyavA.01326.g.A1 PS01550 at 20 mg/mL with 2.5 mM NAD against MCSG1 condition C12, 0.1 M BisTrisHCL pH 6.5, 25% PEG 3350 supplemented with 15% EG as cryo-protectant, crystal tracking ID ...Details: MyavA.01326.g.A1 PS01550 at 20 mg/mL with 2.5 mM NAD against MCSG1 condition C12, 0.1 M BisTrisHCL pH 6.5, 25% PEG 3350 supplemented with 15% EG as cryo-protectant, crystal tracking ID 257485c12, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 2, 2014 / Details: VariMax | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. all: 43895 / Num. obs: 43134 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 32.389 Å2 / Rmerge(I) obs: 0.052 / Χ2: 0.981 / Net I/σ(I): 21.84 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TSC Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2008 / WRfactor Rwork: 0.1727 / FOM work R set: 0.7561 / SU B: 12.315 / SU ML: 0.163 / SU R Cruickshank DPI: 0.1774 / SU Rfree: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 max: 93.1 Å2 / Biso mean: 40.776 Å2 / Biso min: 18.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 16411 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.95→2.001 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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