+Open data
-Basic information
Entry | Database: PDB / ID: 8ayi | ||||||
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Title | Scalindua brodae amxFabZ H48N mutant | ||||||
Components | Beta-hydroxyacyl-(Acyl-carrier-protein) dehydratase | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Candidatus Scalindua brodae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Dietl, A. / Barends, T. | ||||||
Funding support | European Union, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ayi.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ayi.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ayi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/8ayi ftp://data.pdbj.org/pub/pdb/validation_reports/ay/8ayi | HTTPS FTP |
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-Related structure data
Related structure data | 7qv0C 8aybC 8aycC 8aydC 1u1zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Candidatus Scalindua brodae (bacteria) / Gene: SCABRO_02230 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0EHL2 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000001 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS 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) |