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Yorodumi- PDB-8j29: Structures of the C-terminal subenzyme of the malonyl-CoA reducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j29 | ||||||
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Title | Structures of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus | ||||||
Components | Short-chain dehydrogenase/reductase SDR | ||||||
Keywords | OXIDOREDUCTASE / 3-hydroxypropionate(3-HP) / malonyl-CoA reductase / CO2 fixation / short-chain dehydrogenase/reductase (SDR) / Chloroflexus aurantiacus | ||||||
Function / homology | Function and homology information fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Chloroflexus aurantiacus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Ma, Q. / Liu, C. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structures of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus Authors: Ma, Q. / Liu, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j29.cif.gz | 265.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j29.ent.gz | 211.7 KB | Display | PDB format |
PDBx/mmJSON format | 8j29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j29_validation.pdf.gz | 445.2 KB | Display | wwPDB validaton report |
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Full document | 8j29_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 8j29_validation.xml.gz | 26 KB | Display | |
Data in CIF | 8j29_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/8j29 ftp://data.pdbj.org/pub/pdb/validation_reports/j2/8j29 | HTTPS FTP |
-Related structure data
Related structure data | 8j2aC 8j2bC 8j2cC 8j2dC 8j2eC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 73651.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria) Gene: Caur_2614 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9WIU3 |
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#2: Chemical | ChemComp-TLA / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.99 Å3/Da / Density % sol: 58.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: The protein was crystallized in drops containing 1.5 ul protein solution (10 mg/ml) and 1.5 ul reservoir solution (900 mM ammonium tartrate pH 6.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 1.877→72.902 Å / Num. obs: 68842 / % possible obs: 97.7 % / Redundancy: 7 % / CC1/2: 1 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Rsym value: 0.051 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.877→1.883 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 657 / CC1/2: 0.877 / Rpim(I) all: 0.282 / Rrim(I) all: 0.76 / Rsym value: 0.705 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→27.53 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.106
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Displacement parameters | Biso mean: 38.69 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.88→27.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -0.3265 Å / Origin y: 71.5753 Å / Origin z: 57.9217 Å
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Refinement TLS group | Selection details: { A|561 - A|1219 } |