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Open data
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Basic information
Entry | Database: PDB / ID: 8ayi | ||||||
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Title | Scalindua brodae amxFabZ H48N mutant | ||||||
![]() | Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase | ||||||
![]() | LIPID BINDING PROTEIN / Fatty acid biosynthesis | ||||||
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. | ||||||
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 | ![]() | 74 KB | Display | ![]() |
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PDB format | ![]() | 48.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.9 KB | Display | ![]() |
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Full document | ![]() | 431.1 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qv0C ![]() 8aybC ![]() 8aycC ![]() 8aydC ![]() 1u1zS 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
#1: Protein | Mass: 17348.135 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: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.0 M Sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000001 Å / Relative weight: 1 |
Reflection | Resolution: 1.955→31.582 Å / Num. obs: 11349 / % possible obs: 93 % / Redundancy: 6.7 % / Biso Wilson estimate: 61.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.955→2.039 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.437 / Num. unique obs: 568 / CC1/2: 0.271 / % possible all: 43.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1U1Z Resolution: 2.2→31.58 Å / SU ML: 0.2221 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.4907 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: 79.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→31.58 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: -2.03804716567 Å / Origin y: 21.8901085069 Å / Origin z: 5.48572001349 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 1 through 141) |