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Yorodumi- PDB-6do0: Crystal structure of the multidrug binding transcriptional regula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6do0 | |||||||||
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Title | Crystal structure of the multidrug binding transcriptional regulator LmrR in complex with Rhodium Bis-diphosphine Complex | |||||||||
Components | Transcriptional regulator, PadR-like family | |||||||||
Keywords | METAL BINDING PROTEIN / protein scaffold / rhodium bis-diphosphine complex / CO2 hydrogenation | |||||||||
Function / homology | Function and homology information : / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | |||||||||
Biological species | Lactococcus lactis subsp. cremoris (lactic acid bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 Å | |||||||||
Authors | Zadvornyy, O.A. / Laureanti, J.A. / Katipamula, S. / O'Hagan, M. / Peters, J.W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Catalysis / Year: 2019 Title: Protein Scaffold Activates Catalytic CO2 Hydrogenation by a Rhodium Bis(diphosphine) Complex Authors: Laureanti, J.A. / Buckho, G.W. / Katipamula, S. / Su, Q. / Linehan, J.C. / Zadvornyy, O.A. / Peters, J.W. / O'Hagan, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6do0.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6do0.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 6do0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6do0_validation.pdf.gz | 741 KB | Display | wwPDB validaton report |
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Full document | 6do0_full_validation.pdf.gz | 755.7 KB | Display | |
Data in XML | 6do0_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 6do0_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/6do0 ftp://data.pdbj.org/pub/pdb/validation_reports/do/6do0 | HTTPS FTP |
-Related structure data
Related structure data | 3f8bS 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: 13492.228 Da / Num. of mol.: 2 / Mutation: K55D, K59Q, M89C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria) Strain: MG1363 / Gene: llmg_0323 Production host: Lactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria) References: UniProt: A2RI36 #2: Chemical | ChemComp-JY1 / | #3: 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: 2.33 Å3/Da / Density % sol: 47.22 % / Description: needles, plates |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Ammonium acetate in 0.1 M Sodium citrate (pH 6.5), 22% w/v PEG 4000, and 1 mM sodium dithionite PH range: 5.6-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.95 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→39.07 Å / Num. obs: 6343 / % possible obs: 98.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.77 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.034 / Χ2: 0.65 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 922 / CC1/2: 0.918 / Rpim(I) all: 0.212 / Χ2: 0.29 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3f8b Resolution: 2.798→39.068 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 43.91 / 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: 2.798→39.068 Å
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Refine LS restraints |
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LS refinement shell |
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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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