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- PDB-4tw3: Insights into Substrate and Metal Binding from the Crystal Struct... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tw3 | ||||||
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Title | Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Bound | ||||||
![]() | Aldehyde decarbonylase | ||||||
![]() | OXIDOREDUCTASE / non-heme di-iron protein / hydrocarbon production / alpha-helix | ||||||
Function / homology | ![]() aldehyde oxygenase (deformylating) / : / : / transition metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Buer, B.C. / Paul, B. / Das, D. / Stuckey, J.A. / Marsh, E.N.G. | ||||||
![]() | ![]() Title: Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound. Authors: Buer, B.C. / Paul, B. / Das, D. / Stuckey, J.A. / Marsh, E.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.3 KB | Display | ![]() |
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PDB format | ![]() | 83.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 643.4 KB | Display | ![]() |
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Full document | ![]() | 643.7 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pg0C ![]() 4pg1C ![]() 4pgiC ![]() 4pgkC ![]() 2oc5S 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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Unit cell |
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Components
#1: Protein | Mass: 25191.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q7V6D4, aldehyde oxygenase (deformylating) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-STE / | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 1000, 0.1 M HEPES / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38.61 Å / Num. obs: 47171 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 20.98 Å2 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 3 / % possible all: 100 |
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Processing
Software | Name: BUSTER / Version: 2.10.0 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2OC5 Resolution: 1.6→38.61 Å / Cor.coef. Fo:Fc: 0.9577 / Cor.coef. Fo:Fc free: 0.9559 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.064
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Displacement parameters | Biso mean: 22.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.172 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→38.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -20.4648 Å / Origin y: 1.8418 Å / Origin z: -9.5515 Å
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Refinement TLS group | Selection details: { A|21 - A|242 } |