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Yorodumi- PDB-8aer: Malonyl-CoA reductase from Chloroflexus aurantiacus - C-terminal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aer | ||||||||||||
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Title | Malonyl-CoA reductase from Chloroflexus aurantiacus - C-terminal Y731A variant | ||||||||||||
Components | Short-chain dehydrogenase/reductase SDR | ||||||||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / site-directed mutagenesis / 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 / MOLECULAR REPLACEMENT / Resolution: 1.77 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 | 8aer.cif.gz | 268.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aer.ent.gz | 211.7 KB | Display | PDB format |
PDBx/mmJSON format | 8aer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aer_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 8aer_full_validation.pdf.gz | 441.4 KB | Display | |
Data in XML | 8aer_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 8aer_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/8aer ftp://data.pdbj.org/pub/pdb/validation_reports/ae/8aer | HTTPS FTP |
-Related structure data
Related structure data | 8a30SC 8a7sC 8a8tC 8aeoC 8aeqC 8aetC 8aewC S: Starting model for refinement 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: 73229.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aurantiacus J-10-fl (bacteria) Strain: ATCC 29366 / DSM 635 / J-10-fl / Gene: Caur_2614 / Production host: Escherichia coli (E. coli) / References: UniProt: A9WIU3 | ||||
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#2: Chemical | #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: 3.12 Å3/Da / Density % sol: 60.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1 M Sodium citrate tribasic dihydrate, 1 M Ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→48 Å / Num. obs: 156726 / % possible obs: 96.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 34.2 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04429 / Rpim(I) all: 0.0449 / Rrim(I) all: 0.06263 / Net I/σ(I): 9.44 |
Reflection shell | Resolution: 1.77→1.833 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3991 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 15751 / CC1/2: 0.665 / CC star: 0.894 / Rrim(I) all: 0.5644 / Rsym value: 0.3991 / % possible all: 97.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8A30 Resolution: 1.77→48 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→48 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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