- PDB-2x68: The ternary complex of PrnB (the second enzyme in pyrrolnitrin bi... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2x68
Title
The ternary complex of PrnB (the second enzyme in pyrrolnitrin biosynthesis pathway), 7-Cl-L-tryptophan and cyanide
Components
PRNB
Keywords
BIOSYNTHETIC PROTEIN / INDOLAMINE/TRYPTOPHAN DIOXYGENASE SUPERFAMILY
Function / homology
Function and homology information
Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With oxidation of a pair of donors resulting in the reduction of O2 to two molecules of water / tryptophan catabolic process to kynurenine / antibiotic biosynthetic process / oxidoreductase activity / heme binding / metal ion binding Similarity search - Function
Journal: J.Biol.Chem. / Year: 2010 Title: The Ternary Complex of Prnb (the Second Enzyme in Pyrrolnitrin Biosynthesis Pathway), Tryptophan and Cyanide Yields New Mechanistic Insights Into the Indolamine Dioxygenase Superfamily. Authors: Zhu, X. / Van Pee, K.-H. / Naismith, J.H.
History
Deposition
Feb 15, 2010
Deposition site: PDBE / Processing site: PDBE
Revision 1.0
Mar 2, 2010
Provider: repository / Type: Initial release
Revision 1.1
Jul 13, 2011
Group: Advisory / Version format compliance
Revision 1.2
Jul 5, 2017
Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
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Details
Compound details
ENGINEERED RESIDUE IN CHAIN A, CYS 21 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 60 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 21 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 60 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 175 TO SER
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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: 2.9 Å3/Da / Density % sol: 58.1 % / Description: NONE
Resolution: 2.13→24.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.64 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19895
1375
5.2 %
RANDOM
Rwork
0.16485
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obs
0.16661
24910
97.43 %
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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