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- PDB-4dpl: 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: 4dpl | ||||||
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Title | Structure of malonyl-coenzyme A reductase from crenarchaeota in complex with NadP | ||||||
![]() | 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 | ![]() | 575.3 KB | Display | ![]() |
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PDB format | ![]() | 479.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 62.6 KB | Display | |
Data in CIF | ![]() | 88.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dpkC ![]() 4dpmC ![]() 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.: 4 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-NAP / #3: Chemical | ChemComp-UNL / Num. of mol.: 4 / Source method: obtained synthetically #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 33% PEP 426, 0.1 M NaOAc, 0.15 M (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 135044 / Num. obs: 135044 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.067 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.579 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YS4 Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.692 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.116 / 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: 34.979 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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