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Yorodumi- PDB-7mwt: Structure of the E. coli PutA proline dehydrogenase domain (resid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mwt | ||||||
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Title | Structure of the E. coli PutA proline dehydrogenase domain (residues 86-630) complexed with 1,1-Cyclobutanedicarboxylate | ||||||
Components | Bifunctional protein PutA | ||||||
Keywords | OXIDOREDUCTASE / BETA/ALPHA BARREL / FLAVOENZYME / PROLINE CATABOLISM | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / cyclobutane-1,1-dicarboxylic acid / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.19 Å | ||||||
Authors | Tanner, J.J. / Bogner, A.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Org.Biomol.Chem. / Year: 2022 Title: Structure-affinity relationships of reversible proline analog inhibitors targeting proline dehydrogenase. Authors: Bogner, A.N. / 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 | 7mwt.cif.gz | 208.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mwt.ent.gz | 162.5 KB | Display | PDB format |
PDBx/mmJSON format | 7mwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mwt_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7mwt_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7mwt_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 7mwt_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/7mwt ftp://data.pdbj.org/pub/pdb/validation_reports/mw/7mwt | HTTPS FTP |
-Related structure data
Related structure data | 7mwuC 7mwvC 7sqnC 3e2rS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61451.102 Da / Num. of mol.: 1 / Fragment: residues 86-630 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: putA, SAMEA3472047_03659 / Production host: Escherichia coli (E. coli) References: UniProt: A0A383H020, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase |
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-Non-polymers , 6 types, 62 molecules
#2: Chemical | ChemComp-FAD / |
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#3: Chemical | ChemComp-ZPS / |
#4: Chemical | ChemComp-PGE / |
#5: Chemical | ChemComp-PG4 / |
#6: Chemical | ChemComp-SO4 / |
#7: Water | ChemComp-HOH / |
-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: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 20-26% PEG 3350, 50-175 mM sodium citrate, soaked crystals with 50 mM cyclobutane-1,1-dicarboxylic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.19→101.26 Å / Num. obs: 38519 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 53.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.063 / Rrim(I) all: 0.139 / Net I/σ(I): 10.3 / Num. measured all: 183109 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3E2R Resolution: 2.19→70.78 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 31.25 / 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: 158.33 Å2 / Biso mean: 68.6201 Å2 / Biso min: 37.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.19→70.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: 4.9401 Å / Origin y: 49.9337 Å / Origin z: 49.1351 Å
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Refinement TLS group | Selection details: peptide and chain A |