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Yorodumi- PDB-7abn: Structure of the reversible pyrrole-2-carboxylic acid decarboxyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7abn | ||||||
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Title | Structure of the reversible pyrrole-2-carboxylic acid decarboxylase PA0254/HudA | ||||||
Components | UbiD-like decarboxylase | ||||||
Keywords | LIGASE / prFMN / decarboxylase / UbiD / pyrrole / pyrrole-2-carboxylic acid | ||||||
Function / homology | Function and homology information Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / : / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Leys, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2021 Title: Structure and Mechanism of Pseudomonas aeruginosa PA0254/HudA, a prFMN-Dependent Pyrrole-2-carboxylic Acid Decarboxylase Linked to Virulence. Authors: Payne, K.A.P. / Marshall, S.A. / Fisher, K. / Rigby, S.E.J. / Cliff, M.J. / Spiess, R. / Cannas, D.M. / Larrosa, I. / Hay, S. / Leys, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7abn.cif.gz | 423.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7abn.ent.gz | 341 KB | Display | PDB format |
PDBx/mmJSON format | 7abn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/7abn ftp://data.pdbj.org/pub/pdb/validation_reports/ab/7abn | HTTPS FTP |
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-Related structure data
Related structure data | 7aboC 4iwsS 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, 4 molecules DAHM
#1: Protein | Mass: 54564.844 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ECC04_013425 / Production host: Escherichia coli (E. coli) References: UniProt: A0A5F1BUV8, Lyases; Carbon-carbon lyases; Carboxy-lyases |
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-Non-polymers , 5 types, 1440 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-4LU / #5: Chemical | ChemComp-IMD / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.7 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.12 M alcohols, 0.1 M imidazole/MES pH 6.5, 20% v/v glycerol and 10% w/v PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→54 Å / Num. obs: 279939 / % possible obs: 96.4 % / Redundancy: 3.1 % / CC1/2: 1 / Rrim(I) all: 0.093 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.63→1.67 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 18328 / CC1/2: 0.7 / Rrim(I) all: 0.812 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IWS Resolution: 1.65→53.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.25 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.082 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→53.64 Å
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Refine LS restraints |
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