+Open data
-Basic information
Entry | Database: PDB / ID: 5lwl | ||||||||||||
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Title | MaeR D54A mutant response regulator bound to sulfate | ||||||||||||
Components | Transcriptional regulatory protein | ||||||||||||
Keywords | TRANSCRIPTION / Response regulator Beryllium trifluoride Catalytic aspartic acid | ||||||||||||
Function / homology | Function and homology information phosphorelay signal transduction system / DNA-binding transcription factor activity / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Lactobacillus paracasei (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||||||||
Authors | Miguel-Romero, L. / Casino, P. / Landete, J.M. / Monedero, V. / Zuniga, M. / Marina, A. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: Sci Rep / Year: 2017 Title: The malate sensing two-component system MaeKR is a non-canonical class of sensory complex for C4-dicarboxylates. Authors: Miguel-Romero, L. / Casino, P. / Landete, J.M. / Monedero, V. / Zuniga, M. / Marina, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lwl.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lwl.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/5lwl ftp://data.pdbj.org/pub/pdb/validation_reports/lw/5lwl | HTTPS FTP |
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-Related structure data
Related structure data | 5lwkSC 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
#1: Protein | Mass: 13924.093 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus paracasei (bacteria) / Gene: LPL9_2999 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K1MY03, UniProt: A0A247D6V9*PLUS #2: Chemical | #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: 3.93 Å3/Da / Density % sol: 68.67 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 1M lithium sulfate 0.5M ammonium sulfate 0.1M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 21, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97627 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→68.176 Å / Num. all: 7772 / Num. obs: 7772 / % possible obs: 99.2 % / Redundancy: 3.1 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.074 / Rsym value: 0.061 / Net I/av σ(I): 9.5 / Net I/σ(I): 11.2 / Num. measured all: 23722 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LWK Resolution: 3.1→68.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 190.17 Å2 / Biso mean: 116.774 Å2 / Biso min: 49.09 Å2
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Refinement step | Cycle: final / Resolution: 3.1→68.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.181 Å / Total num. of bins used: 20
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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