- PDB-4clm: Structure of Salmonella typhi type I dehydroquinase irreversibly ... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 4clm
Title
Structure of Salmonella typhi type I dehydroquinase irreversibly inhibited with a 1,3,4-trihydroxyciclohexane-1-carboxylic acid derivative
Components
3-DEHYDROQUINATE DEHYDRATASE
Keywords
LYASE / TYPE I DEHYDROQUINASE / INHIBITOR / SHIKIMIS ACID PATHWAY / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information
3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function
: / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details
WPL: THE PROTEIN IS MODIFIED USING AN IRREVERSIBLE INHIBITOR. A THE INHIBITION TAKE PLACE VIA A ...WPL: THE PROTEIN IS MODIFIED USING AN IRREVERSIBLE INHIBITOR. A THE INHIBITION TAKE PLACE VIA A NUCLEOPHILIC RING OPENING OF THE EPOXIDE GROUP OF THE INHIBITOR BY THE NZ-ATOM OF LYS-170 WHICH IS FOLLOWED BY ELIMINATION OF A WATER MOLECULE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.1 Å3/Da / Density % sol: 41.6 % / Description: NONE
Resolution: 1.4→47.21 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.702 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. GAP BY DISORDERED REGION BETWEEN VAL-228 AND ILE-237 IN CHAIN A.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.15498
4293
5 %
RANDOM
Rwork
0.1199
-
-
-
obs
0.12168
81186
95.95 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK