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Yorodumi- PDB-5mg5: A multi-component acyltransferase PhlABC from Pseudomonas protege... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mg5 | ||||||
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Title | A multi-component acyltransferase PhlABC from Pseudomonas protegens soaked with the monoacetylphloroglucinol (MAPG) | ||||||
Components |
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Keywords | TRANSFERASE / acyltransferase / Pseudomonas protegens / PhlABC / multi-component / MAPG | ||||||
Function / homology | Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / acyltransferase activity, transferring groups other than amino-acyl groups / Thiolase-like / benzene-1,3,5-triol / : / : / 2,4-diacetylphloroglucinol biosynthesis protein PhlC Function and homology information | ||||||
Biological species | Pseudomonas protegens (bacteria) Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 Å | ||||||
Authors | Pavkov-Keller, T. / Schmidt, N.G. / Kroutil, W. / Gruber, K. | ||||||
Citation | Journal: Chembiochem / Year: 2019 Title: Structure and Catalytic Mechanism of a Bacterial Friedel-Crafts Acylase. Authors: Pavkov-Keller, T. / Schmidt, N.G. / Zadlo-Dobrowolska, A. / Kroutil, W. / Gruber, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mg5.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5mg5.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5mg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mg5_validation.pdf.gz | 626.3 KB | Display | wwPDB validaton report |
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Full document | 5mg5_full_validation.pdf.gz | 714.9 KB | Display | |
Data in XML | 5mg5_validation.xml.gz | 232.4 KB | Display | |
Data in CIF | 5mg5_validation.cif.gz | 314.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mg5 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mg5 | HTTPS FTP |
-Related structure data
Related structure data | 5m3kSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ADGJMPSV
#1: Protein | Mass: 38565.480 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas protegens (bacteria) / Gene: CEP86_09500 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Z3SPL2 |
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-2,4-diacetylphloroglucinol biosynthesis ... , 2 types, 16 molecules BEHKNQTWCFILORUX
#2: Protein | Mass: 16666.434 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas protegens (bacteria) / Gene: CEP86_09490 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Z3SPP2 #3: Protein | Mass: 42581.941 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria) Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: phlC, PFL_5955 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4K420 |
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-Non-polymers , 3 types, 74 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-13X / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: Index screen #55 (0.05 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 0% v/v Polyethylene glycol monomethyl ether 550). 12mg/ml in potassium phosphate buffer, 50 mM, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.95 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 3.44→49.72 Å / Num. obs: 99724 / % possible obs: 99 % / Redundancy: 6 % / CC1/2: 0.97 / Rmerge(I) obs: 0.268 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3.44→3.56 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.57 / CC1/2: 0.81 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M3K Resolution: 3.44→49.725 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.44→49.725 Å
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Refine LS restraints |
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LS refinement shell |
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