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Yorodumi- PDB-8j2d: Structure of the C-terminal subenzyme of the malonyl-CoA reductas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j2d | ||||||
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Title | Structure of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus, mutant N940V/K1106W/S1114R in complex with NADP+ | ||||||
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: 2.21 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 | 8j2d.cif.gz | 264.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j2d.ent.gz | 210.5 KB | Display | PDB format |
PDBx/mmJSON format | 8j2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j2d_validation.pdf.gz | 791.5 KB | Display | wwPDB validaton report |
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Full document | 8j2d_full_validation.pdf.gz | 796.5 KB | Display | |
Data in XML | 8j2d_validation.xml.gz | 24 KB | Display | |
Data in CIF | 8j2d_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/8j2d ftp://data.pdbj.org/pub/pdb/validation_reports/j2/8j2d | HTTPS FTP |
-Related structure data
Related structure data | 8j29C 8j2aC 8j2bC 8j2cC 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
#1: Protein | Mass: 73764.039 Da / Num. of mol.: 1 / Mutation: N940V/K1106W/S1114R 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-NAP / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: The protein in complex with NADP+ was crystallized in drops containing 1.5 ul protein solution (10 mg/ml protein+1.7 mM NADP disodium salt, incubated at 4 degrees for 1 h) and 1.5 ul ...Details: The protein in complex with NADP+ was crystallized in drops containing 1.5 ul protein solution (10 mg/ml protein+1.7 mM NADP disodium salt, incubated at 4 degrees for 1 h) and 1.5 ul reservoir solution (100 mM sodium citrate pH 5.0, 150 mM sodium citrate, 16% w/v PEG3350). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97876 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97876 Å / Relative weight: 1 |
Reflection | Resolution: 2.205→75.846 Å / Num. obs: 43280 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Rsym value: 0.077 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.205→2.243 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2146 / CC1/2: 0.841 / Rpim(I) all: 0.318 / Rrim(I) all: 0.847 / Rsym value: 0.785 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→32.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.173
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Displacement parameters | Biso mean: 58.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.21→32.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -37.4451 Å / Origin y: 7.7494 Å / Origin z: -14.6344 Å
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Refinement TLS group | Selection details: { A|562 - A|1219 } |