- PDB-2y30: Simocyclinone D8 bound form of TetR-like repressor SimR -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2y30
Title
Simocyclinone D8 bound form of TetR-like repressor SimR
Components
PUTATIVE REPRESSOR SIMREG2
Keywords
TRANSCRIPTION / TETR-FAMILY
Function / homology
Function and homology information
transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / metal ion binding Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details
SIMOCYCLINONE D8 (SM8): ADDED TO PROTEIN PRIOR TO CRYSTALLIZATION
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Experimental details
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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 % / Description: NONE
Crystal grow
Method: vapor diffusion, hanging drop / pH: 4.6 Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT 5MG/ML PLUS EXCESS LIGAND IN 25MM TRIS-HCL PH8.4, 300MM NACL MIXED WITH 25% PEG 1000, 0.1M SODIUM ACETATE PH4.6 IN 1 TO 1 RATIO
Resolution: 2.3→73.68 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.88 / SU B: 7.339 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27001
1227
5.1 %
RANDOM
Rwork
0.19966
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obs
0.20326
22723
96.94 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK