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Yorodumi- PDB-7na0: Structure of Geobacter sulfurreducens proline utilization A (PutA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7na0 | ||||||
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Title | Structure of Geobacter sulfurreducens proline utilization A (PutA) variant A206W | ||||||
Components | Bifunctional protein PutA | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME | ||||||
Function / homology | Function and homology information proline dehydrogenase activity / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / L-glutamate gamma-semialdehyde dehydrogenase / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacter sulfurreducens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Tanner, J.J. / Korasick, D.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2021 Title: Probing the function of a ligand-modulated dynamic tunnel in bifunctional proline utilization A (PutA). Authors: Korasick, D.A. / Christgen, S.L. / Qureshi, I.A. / Becker, D.F. / Tanner, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7na0.cif.gz | 787.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7na0.ent.gz | 640.7 KB | Display | PDB format |
PDBx/mmJSON format | 7na0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/7na0 ftp://data.pdbj.org/pub/pdb/validation_reports/na/7na0 | HTTPS FTP |
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-Related structure data
Related structure data | 4nm9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 112439.805 Da / Num. of mol.: 2 / Mutation: A206W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (bacteria) Strain: ATCC 51573 / DSM 12127 / PCA / Gene: putA, GSU3395 / Production host: Escherichia coli (E. coli) References: UniProt: Q746X3, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | 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: 2.82 Å3/Da / Density % sol: 56.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.05 M ammonium sulfate, 0.05 M BIS-TRIS pH 6.5, and 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Feb 20, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→58.52 Å / Num. obs: 386519 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.057 / Rrim(I) all: 0.152 / Net I/σ(I): 13.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4NM9 Resolution: 1.9→56.181 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 19.6 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.17 Å2 / Biso mean: 21.4417 Å2 / Biso min: 7.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→56.181 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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