- PDB-4q12: Crystal structure of a putative uncharacterized protein Rv3404c a... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4q12
Title
Crystal structure of a putative uncharacterized protein Rv3404c and likely sugar N-formyltransferase from Mycobacterium tuberculosis bound to uridine diphosphate
Components
Uncharacterized protein Rv3404c/MT3512
Keywords
TRANSFERASE / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / National Institute for Allergy and Infectious Diseases / cell wall biogenesis / sugar formyl transferase / Structural Genomics
Function / homology
Function and homology information
Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases / conversion of methionyl-tRNA to N-formyl-methionyl-tRNA / hydroxymethyl-, formyl- and related transferase activity / methionyl-tRNA formyltransferase activity / biosynthetic process / carbohydrate metabolic process / protein homodimerization activity / cytosol Similarity search - Function
Journal: To be Published Title: Crystal structure of a putative uncharacterized protein Rv3404c and likely sugar N-formyltransferase from Mycobacterium tuberculosis Authors: Edwards, T.E. / Dranow, D.M.
Mass: 18.015 Da / Num. of mol.: 190 / 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 / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 7.24 Å3/Da / Density % sol: 83.01 %
Crystal grow
Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MytuD.17389.a.A1.PW30616 at 19 mg/mL with 2 mM UDP against CHST screen condition E1, 2.0 M NaCl, 10% PEG 6000 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 253215e1, ...Details: MytuD.17389.a.A1.PW30616 at 19 mg/mL with 2 mM UDP against CHST screen condition E1, 2.0 M NaCl, 10% PEG 6000 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 253215e1, unique puck ID tbx9-1, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.1731 / WRfactor Rwork: 0.1513 / FOM work R set: 0.8837 / SU B: 11.877 / SU ML: 0.119 / SU R Cruickshank DPI: 0.21 / SU Rfree: 0.1812 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1937
1930
4.8 %
RANDOM
Rwork
0.1715
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obs
0.1725
40056
99.96 %
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all
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40080
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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
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