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- PDB-4rc5: Crystal structure of cyanobacterial aldehyde-deformylating oxygenase -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rc5 | ||||||
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Title | Crystal structure of cyanobacterial aldehyde-deformylating oxygenase | ||||||
![]() | (Aldehyde decarbonylase) x 2 | ||||||
![]() | LYASE / oxygenase | ||||||
Function / homology | ![]() aldehyde oxygenase (deformylating) activity / aldehyde oxygenase (deformylating) / : / : / transition metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jia, C.J. / Li, M. / Chang, W.R. | ||||||
![]() | ![]() Title: Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases. Authors: Jia, C. / Li, M. / Li, J. / Zhang, J. / Zhang, H. / Cao, P. / Pan, X. / Lu, X. / Chang, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.5 KB | Display | ![]() |
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PDB format | ![]() | 79.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 453.1 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4quwSC ![]() 4rc6C ![]() 4rc7C ![]() 4rc8C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 25284.721 Da / Num. of mol.: 1 / Fragment: UNP residues 11-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7942 / Gene: Synpcc7942_1593 / Production host: ![]() ![]() References: UniProt: Q54764, aldehyde oxygenase (deformylating) | ||||
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#2: Protein | Mass: 25397.879 Da / Num. of mol.: 1 / Fragment: UNP residues 10-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7942 / Gene: Synpcc7942_1593 / Production host: ![]() ![]() References: UniProt: Q54764, aldehyde oxygenase (deformylating) | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.2M L-proline, 0.1M Hepes, 25%(w/v) PEG1500, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 21892 / Num. obs: 21848 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.34 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QUW Resolution: 2.3→43.944 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.051 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→43.944 Å
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Refine LS restraints |
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