- PDB-5hsq: The surface engineered photosensory module (PAS-GAF-PHY) of the b... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5hsq
Title
The surface engineered photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A.
Components
Bacteriophytochrome protein
Keywords
SIGNALING PROTEIN / surface mutations / bilin chromophore / photoisomerization
Function / homology
Function and homology information
red or far-red light photoreceptor activity / red, far-red light phototransduction / osmosensory signaling via phosphorelay pathway / protein histidine kinase activity / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / metal ion binding Similarity search - Function
PHY domain / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain ...PHY domain / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 54736.945 Da / Num. of mol.: 1 / Mutation: E86A, E87A, E336A, K337A Source method: isolated from a genetically manipulated source Details: The residue numbering in the PDB entry differs from the one shown in this sequence alignment. The first residue in the PDB entry is 'Leu17' in accordance with the sequence for the entry ...Details: The residue numbering in the PDB entry differs from the one shown in this sequence alignment. The first residue in the PDB entry is 'Leu17' in accordance with the sequence for the entry AAT99575 (NCBI). The respective numbering was used in a number of publications on this protein, and we did not change it in this entry for the sake of consistency with published work and because the true N-terminus has not yet been identified at the protein level. Source: (gene. exp.) Agrobacterium fabrum (bacteria) / Strain: C58 / ATCC 33970 / Gene: Atu1990 / Plasmid: pET21b(+) Details (production host): The coding sequence of the protein of interest was subcloned using NdeI and XhoI sites of the plasmid. Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7CY45
Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 2.59 Å3/Da / Density % sol: 52.6 % / Description: Bipyramidal
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.03 M diethyleneglycol, 0.03 M triethyleneglycol, 0.03 M tetraethyleneglycol, 0.03 M pentaethyleneglycol, 20% glycerol, 10% PEG8000, 0.05 M MES, 0.05 M imidazole pH 6.5
Resolution: 1.85→34.31 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.454 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22371
2528
5.1 %
RANDOM
Rwork
0.18269
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obs
0.18474
46971
97.96 %
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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