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Open data
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Basic information
Entry | Database: PDB / ID: 8ayb | ||||||
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Title | anammox-specific FabZ from Scalindua brodae | ||||||
![]() | Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase | ||||||
![]() | BIOSYNTHETIC PROTEIN / ladderane / lipid biosynthesis / dehydratase | ||||||
Function / homology | Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / HotDog domain superfamily / Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dietl, A. / Barends, T.R.M. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Structures of an unusual 3-hydroxyacyl dehydratase (FabZ) from a ladderane-producing organism with an unexpected substrate preference. Authors: Dietl, A. / Wellach, K. / Mahadevan, P. / Mertes, N. / Winter, S.L. / Kutsch, T. / Walz, C. / Schlichting, I. / Fabritz, S. / Barends, T.R.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.2 KB | Display | ![]() |
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PDB format | ![]() | 49.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424 KB | Display | ![]() |
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Full document | ![]() | 425.4 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 9.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qv0C ![]() 8aycC ![]() 8aydC ![]() 8ayiC ![]() 1uizS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15554.169 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.6 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033217 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 15501 / % possible obs: 96.1 % / Redundancy: 9.1 % / Biso Wilson estimate: 35.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2237 / CC1/2: 0.847 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UIZ Resolution: 1.8→39.66 Å / SU ML: 0.1724 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.1664 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→39.66 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -1.97843532239 Å / Origin y: 21.8411875824 Å / Origin z: 5.58195911304 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 1 through 141) |