- PDB-1d0v: CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIM... -
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Basic information
Entry
Database: PDB / ID: 1d0v
Title
CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH ITS REACTION PRODUCTS DETERMINED TO 1.9 A RESOLUTION
Journal: Biochemistry / Year: 1999 Title: The three-dimensional structures of nicotinate mononucleotide:5,6- dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella typhimurium complexed with 5,6-dimethybenzimidazole ...Title: The three-dimensional structures of nicotinate mononucleotide:5,6- dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella typhimurium complexed with 5,6-dimethybenzimidazole and its reaction products determined to 1.9 A resolution. Authors: Cheong, C.G. / Escalante-Semerena, J.C. / Rayment, I.
History
Deposition
Sep 14, 1999
Deposition site: RCSB / Processing site: RCSB
Revision 1.0
Dec 29, 1999
Provider: repository / Type: Initial release
Revision 1.1
Apr 27, 2008
Group: Version format compliance
Revision 1.2
Jul 13, 2011
Group: Derived calculations / Version format compliance
Mass: 18.015 Da / Num. of mol.: 158 / 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: 2
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Sample preparation
Crystal
Density Matthews: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.3 NH4H2PO4/(NH4)2HPO4, 1MM 5,6-DIMETHYLBENZIMIDAZOLE, 4 % POLYETHYLENEGLYCOL, AND THEN THE CRYSTALS WERE SOAKED IN 21 MM NICOTINATE MONONUCLEOTIDE IN 1.0 M NAH2PO4/K2HPO4 (PH 6.0), VAPOR ...Details: 1.3 NH4H2PO4/(NH4)2HPO4, 1MM 5,6-DIMETHYLBENZIMIDAZOLE, 4 % POLYETHYLENEGLYCOL, AND THEN THE CRYSTALS WERE SOAKED IN 21 MM NICOTINATE MONONUCLEOTIDE IN 1.0 M NAH2PO4/K2HPO4 (PH 6.0), VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Density % sol: 42 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
ID
Conc.
Common name
Crystal-ID
Sol-ID
1
6mg/ml
protein
1
drop
2
1.3M
ammoniumphosphate
1
reservoir
3
1mM
DMB
1
reservoir
4
4 %
PEG400
1
reservoir
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
277
1
2
274
1
Diffraction source
Source
Type
ID
Wavelength
ROTATING ANODE
ENRAF-NONIUS
1
1.5418
2
Detector
Type
ID
Detector
Date
SIEMENS HI-STAR
1
AREA DETECTOR
Jan 20, 1999
2
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 1.9→30 Å / Num. all: 25069 / Num. obs: 21894 / % possible obs: 87.33 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.9
Reflection shell
Resolution: 1.88→1.98 Å / Redundancy: 1.3 % / % possible all: 65
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