+Open data
-Basic information
Entry | Database: PDB / ID: 7x5j | ||||||
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Title | ACP-dependent oxoacyl reductase | ||||||
Components | 3-oxoacyl-ACP reductase | ||||||
Keywords | OXIDOREDUCTASE / reductase / fatty acid biosynthesis / hexamer / combineding with NADP+ | ||||||
Function / homology | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHENYLALANINE Function and homology information | ||||||
Biological species | Candidatus Methanoliparum (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wang, S. / Bai, L. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: ACP-dependent oxoacyl reductase Authors: Wang, S. / Bai, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x5j.cif.gz | 576.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x5j.ent.gz | 469 KB | Display | PDB format |
PDBx/mmJSON format | 7x5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x5j_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7x5j_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7x5j_validation.xml.gz | 57.8 KB | Display | |
Data in CIF | 7x5j_validation.cif.gz | 81.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/7x5j ftp://data.pdbj.org/pub/pdb/validation_reports/x5/7x5j | HTTPS FTP |
-Related structure data
Related structure data | 3osuS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 27307.080 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Methanoliparum (archaea) / Production host: Eschenbachia (plant) #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-PHE / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 20%(v/v) Butanediol, 0.1 M Sodium acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2021 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.1→152.37 Å / Num. obs: 105199 / % possible obs: 97.9 % / Redundancy: 13.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.086 / Rrim(I) all: 0.229 / Net I/σ(I): 7.1 | ||||||||||||||||||
Reflection shell | Num. unique obs: 105218 / Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OSU Resolution: 2.1→97.275 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.208 / SU B: 6.152 / SU ML: 0.151 / Average fsc free: 0.8428 / Average fsc work: 0.8595 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.186 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→97.275 Å
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Refine LS restraints |
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LS refinement shell |
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