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- PDB-4dpm: Structure of malonyl-coenzyme A reductase from crenarchaeota in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dpm | ||||||
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Title | Structure of malonyl-coenzyme A reductase from crenarchaeota in complex with CoA | ||||||
![]() | Malonyl-CoA/succinyl-CoA reductase | ||||||
![]() | OXIDOREDUCTASE / dinucleotide binding / dimerization domain / reductase / NadP / CoA | ||||||
Function / homology | ![]() malonyl-CoA reductase (malonate semialdehyde-forming) / aspartate-semialdehyde dehydrogenase activity / threonine biosynthetic process / methionine biosynthetic process / NAD binding / NADP binding / protein dimerization activity / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Demmer, U. / Warkentin, E. / Srivastava, A. / Kockelkorn, D. / Fuchs, G. / Ermler, U. | ||||||
![]() | ![]() Title: Structural Basis for a Bispecific NADP+ and CoA Binding Site in an Archaeal Malonyl-Coenzyme A Reductase. Authors: Demmer, U. / Warkentin, E. / Srivastava, A. / Kockelkorn, D. / Potter, M. / Marx, A. / Fuchs, G. / Ermler, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 857.2 KB | Display | ![]() |
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PDB format | ![]() | 722.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 91.3 KB | Display | |
Data in CIF | ![]() | 121.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dpkC ![]() 4dplC ![]() 1ys4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 39609.727 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q96YK1, malonyl-CoA reductase (malonate semialdehyde-forming), succinate-semialdehyde dehydrogenase (acylating) #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-COA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 11% PEG 6000, 10 mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 108682 / Num. obs: 108682 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.069 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.3→2.36 Å / Rsym value: 0.49 / % possible all: 54.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YS4 Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.025 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 84.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 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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