- PDB-2y31: Simocyclinone C4 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: 2y31
Title
Simocyclinone C4 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.: 277 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
POLYETHYLENE GLYCOL (PG4): COMPONENT OF PRECIPITANT. SIMOCYCLINONE C4 (SMQ): ADDED TO PROTEIN PRIOR ...POLYETHYLENE GLYCOL (PG4): COMPONENT OF PRECIPITANT. SIMOCYCLINONE C4 (SMQ): 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: 3.13 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal grow
Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT 5MG/ML PLUS EXCESS LIGAND IN 25MM TRIS-HCL PH8.4, 300MM NACL MIXED WITH 28% PEG 400, 0.2M CALCIUM CHLORIDE 0.1M HEPES PH7.5 IN 1 TO 1 RATIO
Resolution: 2.3→74.97 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.849 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.21 / 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
0.24612
1726
5 %
RANDOM
Rwork
0.19776
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obs
0.20019
32723
96.34 %
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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