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Yorodumi- PDB-7q34: Crystal structure of the multidrug binding transcriptional regula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q34 | ||||||||||||
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Title | Crystal structure of the multidrug binding transcriptional regulator LmrR in complex squaraine dye | ||||||||||||
Components | Helix-turn-helix transcriptional regulator | ||||||||||||
Keywords | FLUORESCENT PROTEIN / artificial fluorescent proteins / color down-conversion / deep-red biophosphors / bio-hybrid light emitting diodes | ||||||||||||
Function / homology | Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Chem-8TF / NICKEL (II) ION / Helix-turn-helix transcriptional regulator Function and homology information | ||||||||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||||||||
Authors | Liutkus, M. / Mejias, S.H. / Barolo, C. / Cortajarena, A.L. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: Adv Funct Mater / Year: 2022 Title: Designing Artificial Fluorescent Proteins: Squaraine-LmrR Biophosphors for High Performance Deep-Red Biohybrid Light-Emitting Diodes Authors: Ferrara, S. / Mejias, S.H. / Liutkus, M. / Renno, G. / Stella, F. / Kociolek, I. / Fuenzalida-Werner, J.P. / Barolo, C. / Coto, P.B. / Cortajarena, A.L. / Costa, R.D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q34.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q34.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 7q34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q34_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7q34_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7q34_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 7q34_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/7q34 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/7q34 | HTTPS FTP |
-Related structure data
Related structure data | 3f8bS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 14891.720 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Gene: CYU10_001323, D4M07_02500, E34_1323, FEZ45_05535, FIB48_07105, GJI88_04795, HPC60_09780, JCM5805K_2657, KF282_0527, LKF24_1179, LKF67_0238, LL14B4_01620, LL275_0346, LLUC06_0422, LLUC08_0288, ...Gene: CYU10_001323, D4M07_02500, E34_1323, FEZ45_05535, FIB48_07105, GJI88_04795, HPC60_09780, JCM5805K_2657, KF282_0527, LKF24_1179, LKF67_0238, LL14B4_01620, LL275_0346, LLUC06_0422, LLUC08_0288, LLUC11_0290, LMG8520_0357, LMG9449_1101, N42_0245, VN91_0116 Plasmid: pET-17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A0A7SZD7 #2: Chemical | ChemComp-NI / #3: Chemical | 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: 2.56 Å3/Da / Density % sol: 51.97 % / Description: blue cubes |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Hepes, pH 7.5, 5 mM NiCl2, 5 mM MgCl2, 5 mM CdCl2, 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.48459 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.48459 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→100.429 Å / Num. all: 19703 / Num. obs: 19703 / % possible obs: 100 % / Redundancy: 11.5 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.159 / Rsym value: 0.144 / Net I/av σ(I): 1.7 / Net I/σ(I): 9.4 / Num. measured all: 226610 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.408
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3f8b Resolution: 2.6→64.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.891 / SU B: 16.945 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.484 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 174.12 Å2 / Biso mean: 84.846 Å2 / Biso min: 39.2 Å2
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Refinement step | Cycle: final / Resolution: 2.6→64.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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