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Yorodumi- PDB-8a30: Malonyl-CoA reductase from Chloroflexus aurantiacus - C-terminal Apo -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a30 | ||||||||||||
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Title | Malonyl-CoA reductase from Chloroflexus aurantiacus - C-terminal Apo | ||||||||||||
Components | Short-chain dehydrogenase/reductase SDR | ||||||||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / bi-functional enzyme / reductase / malonyl-CoA / 3-hydroxypropionate / 3-HP cycle | ||||||||||||
Function / homology | fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / Short-chain dehydrogenase/reductase SDR Function and homology information | ||||||||||||
Biological species | Chloroflexus aurantiacus J-10-fl (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||||||||
Authors | Kabasakal, B.V. / Murray, J.W. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Biochimie / Year: 2023 Title: Dynamic lid domain of Chloroflexus aurantiacus Malonyl-CoA reductase controls the reaction. Authors: Kabasakal, B.V. / Cotton, C.A.R. / Murray, J.W. #1: Journal: Biorxiv / Year: 2023 Title: Dynamic lid domain of Chloroflexus aurantiacus Malonyl-CoA Reductase controls the reaction Authors: Kabasakal, B.V. / Cotton, C.A.R. / Murray, J.W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a30.cif.gz | 293.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a30.ent.gz | 232.2 KB | Display | PDB format |
PDBx/mmJSON format | 8a30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a30_validation.pdf.gz | 416.2 KB | Display | wwPDB validaton report |
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Full document | 8a30_full_validation.pdf.gz | 416.7 KB | Display | |
Data in XML | 8a30_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 8a30_validation.cif.gz | 44.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/8a30 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/8a30 | HTTPS FTP |
-Related structure data
Related structure data | 8a7sC 8a8tC 8aeoC 8aeqC 8aerC 8aetC 8aewC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 73321.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aurantiacus J-10-fl (bacteria) Gene: Caur_2614 / Production host: Escherichia coli (E. coli) / References: UniProt: A9WIU3 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M Succinic acid, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→55.5 Å / Num. obs: 154410 / % possible obs: 99.36 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.09 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.04132 / Rpim(I) all: 0.04132 / Rrim(I) all: 0.05843 / Net I/av σ(I): 9.93 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 1.8 % / Rmerge(I) obs: 1.441 / Num. unique obs: 15025 / CC1/2: 0.203 / CC star: 0.581 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→55.5 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→55.5 Å
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Refine LS restraints |
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LS refinement shell |
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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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