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1d0v

CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH ITS REACTION PRODUCTS DETERMINED TO 1.9 A RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 76.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE

OrganismNot specified

UniProt Q05603

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–356 Not recorded RBZ ALPHA-RIBAZOLE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；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 Resolution 1.90 Å R-free 0.249

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1D0V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D0S CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE : 5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH 5, 6-DIMETHYLBENZIMIDAZOLE Deposited 1999-09-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 2 DMD 5,6-DIMETHYLBENZIMIDAZOLE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；1.3 M NH4H2PO4/(NH4)2HPO4, 1 MM 5,6-DIMETHYLBENZIMIDAZOLE, 4 % POLYETHYLENEGLYCOL 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP
Resolution 1.90 Å
1JH8 Structural Investigation of the Biosynthesis of Alternative Lower Ligands for Cobamides by Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase (CobT) from Salmonella enterica Deposited 2001-06-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 4 ADE ADENINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；1.4 M Ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.256
1JHA Structural Investigation of the Biosynthesis of Alternative Lower Ligands for Cobamides by Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase (CobT) from Salmonella enterica Deposited 2001-06-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded AAM ALPHA-ADENOSINE MONOPHOSPHATE × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.275
1JHM Three-dimensional Structure of CobT in Complex with 5-methylbenzimidazole Deposited 2001-06-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 4 5MB 5-METHYLBENZIMIDAZOLE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.302
1JHO Three-dimensional Structure of CobT in Complex with the Reaction Products of 5-methylbenzimidazole and NaMN Deposited 2001-06-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded RMB N1-(5'-PHOSPHO-ALPHA-RIBOSYL)-5-METHYLBENZIMIDAZOLE × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.256
1JHP Three-dimensional Structure of CobT in Complex with 5-methoxybenzimidazole Deposited 2001-06-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 4 5OB 5-METHOXYBENZIMIDAZOLE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.295
1JHQ Three-dimensional Structure of CobT in Complex with Reaction Products of 5-methoxybenzimidazole and NaMN Deposited 2001-06-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PMO N1-(5'-PHOSPHO-ALPHA-RIBOSYL)-5-METHOXYBENZIMIDAZOLE × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.279
1JHR Three-dimensional Structure of CobT in Complex with Reaction Products of 2-hydroxypurine and NaMN Deposited 2001-06-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded NIO NICOTINIC ACID × 2 P2P N7-(5'-PHOSPHO-ALPHA-RIBOSYL)-2-HYDROXYPURINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.259
1JHU Three-dimensional Structure of CobT in Complex with p-cresol Deposited 2001-06-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 4 PCR P-CRESOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.284
1JHV Three-dimensional Structure of CobT in Complex with p-cresol and Nicotinate Deposited 2001-06-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 2 PCR P-CRESOL × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.274
1JHX Three-dimensional Structure of CobT in Complex with Phenol Deposited 2001-06-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 4 IPH PHENOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.267
1JHY Three-dimensional Structure of CobT in Complex with Phenol and Nicotinate Deposited 2001-06-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 2 IPH PHENOL × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.264
1L4B Crystal Structure of CobT in apo state Deposited 2002-03-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 1.70 Å R-free 0.218
1L4E The crystal structure of CobT complexed with alpha-ribazole-5'-phosphate Deposited 2002-03-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded RBZ ALPHA-RIBAZOLE-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate at pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.218
1L4F The crystal structure of CobT complexed with 4,5-dimethyl-1,2-phenylenediamine and nicotinate mononucleotide Deposited 2002-03-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded 150 4,5-DIMETHYL-1,2-PHENYLENEDIAMINE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.10 Å R-free 0.221
1L4G Crystal Structure of CobT complexed with 4-methylcatechol and nicotinate mononucleotide Deposited 2002-03-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded MCT 4-METHYLCATECHOL × 2 NCN NICOTINATE MONONUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.10 Å R-free 0.226
1L4H Crystal Structure of CobT complexed with indole and nicotinate mononucleotide Deposited 2002-03-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded IND INDOLE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.10 Å R-free 0.209
1L4K Crystal Structure of CobT complexed with 3,4-dimethylaniline and nicotinate mononucleotide Deposited 2002-03-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded 34A 3,4-DIMETHYLANILINE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.20 Å R-free 0.207
1L4L Crystal Structure of CobT complexed with 2,5-dimethylaniline and nicotinate mononucleotide Deposited 2002-03-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded XYD 2,5-DIMETHYLANILINE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.202
1L4M Crystal Structure of CobT complexed with 2-amino-p-cresol and nicotinate mononucleotide Deposited 2002-03-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded 2AC 2-AMINO-P-CRESOL × 2 NCN NICOTINATE MONONUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.216
1L4N Crystal Structure of CobT complexed with 2-aminophenol Deposited 2002-03-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 2 2AF 2-AMINOPHENOL × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.199
1L5F Crystal Structure of CobT complexed with benzimidazole Deposited 2002-03-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 4 BZI BENZIMIDAZOLE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 1.90 Å R-free 0.215
1L5K Crystal Structure of CobT complexed with N1-(5'-phosphoribosyl)-benzimidazole and nicotinate Deposited 2002-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded 1RB 1-ALPHA-D-RIBOFURANOSYL-BENZIMIAZOLE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.216
1L5L Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)purine and nicotinate Deposited 2002-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded 7RP 7-ALPHA-D-RIBOFURANOSYL-PURINE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.197
1L5M Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)-2-aminopurine and nicotinate Deposited 2002-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded 7RA 7-ALPHA-D-RIBOFURANOSYL-2-AMINOPURINE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.218
1L5N Crystal Structure of CobT complexed with imidazole Deposited 2002-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded PO4 PHOSPHATE ION × 2 IMD IMIDAZOLE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 1.90 Å R-free 0.200
1L5O Crystal Structure of CobT complexed with 3,4-dimethylphenol and nicotinate mononucleotide Deposited 2002-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Not recorded 2MP 3,4-DIMETHYLPHENOL × 2 NCN NICOTINATE MONONUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 1.60 Å R-free 0.199
4KQF Crystal structure of CobT E174A complexed with adenine Deposited 2013-05-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Mutation：E174A SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 ADE ADENINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；1.05 M ammonium sulfate, 0.1 M MES, 5% glycerol, pH 6.0, VAPOR DIFFUSION, temperature 298K
Resolution 1.90 Å R-free 0.223
4KQG Crystal structure of CobT E174A complexed with DMB Deposited 2013-05-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Mutation：E174A PO4 PHOSPHATE ION × 2 DMD 5,6-DIMETHYLBENZIMIDAZOLE × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；10% MEPEG 5000, 0.1 M MES, 0.2 M ammonium sulfate, 5% glycerol, pH 6.0, VAPOR DIFFUSION, temperature 298K
Resolution 1.90 Å R-free 0.225
4KQH Crystal structure of CobT E317A Deposited 2013-05-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Mutation：E317A SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；20% PEG 1500, 0.1 M MES, 0.05M lithium sulfate, 2.5% ethylene glycol, pH 6.0, VAPOR DIFFUSION, temperature 298K
Resolution 1.90 Å R-free 0.225
4KQI Crystal structure of CobT E317A complexed with its reaction products Deposited 2013-05-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Mutation：E317A RBZ ALPHA-RIBAZOLE-5'-PHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 2 NIO NICOTINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；20% PEG 1500, 0.1 M MES, 0.05 M lithium sulfate, 2.5% ethylene glycol, pH 6.0, VAPOR DIFFUSION, temperature 298K
Resolution 1.40 Å R-free 0.195
4KQJ Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN Deposited 2013-05-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Mutation：S80Y, Q88M, L175M NCN NICOTINATE MONONUCLEOTIDE × 2 PCR P-CRESOL × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 9；298 K；24% MEPEG 5000, 0.1 M CHES, 0.05 M magnesium sulfate, 5 mM p-cresol, 1% DMSO, 5% ethylene glycol, pH 9.0, VAPOR DIFFUSION, temperature 298K
Resolution 1.95 Å R-free 0.223
4KQK Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol Deposited 2013-05-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–356（356 aa）
Chain B 1–356（356 aa）
Mutation：S80Y, Q88M, L175M Mutation：S80Y, Q88M, L175M SO4 SULFATE ION × 4 PCR P-CRESOL × 2 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 9；298 K；24% MEPEG 5000, 0.1 M CHES, 0.05 M magnesium sulfate, 5 mM p-cresol, 1% DMSO, 20% ethylene glycol, pH 9.0, VAPOR DIFFUSION, temperature 298K
Resolution 1.47 Å R-free 0.195

33 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COBT_SALTY
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–356； UniProt 1–356

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1d0v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d0v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d0v
Deposition date deposition_date1999-09-14
Structure title titleCRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH ITS REACTION PRODUCTS DETERMINED TO 1.9 A RESOLUTION
Keywords keywordsDINUCLEOTIDE-BINDING MOTIF, PHOSPHORIBOSYLTRANSFERASE, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.91 Å
Radius of gyration Rg (electron density) rg_electron20.16 Å
Forward intensity I(0) i021320200.00
Molecular weight molecular_weight35101.0 kDa
Excluded volume excluded_volume43919 ų
Envelope volume envelope_volume49020 ų
Hydration-shell volume shell_volume20835 ų
Envelope diameter envelope_diameter76.6 Å
Shell Rg shell_rg26.27 Å
Envelope Rg envelope_rg20.76 Å
Shape Rg shape_rg20.20 Å
Total Rg total_rg20.83 Å
Total atoms total_atoms2451
Residues n_residues346
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax76.1 Å
Rg (real space) rg_real20.96 Å
Rg uncertainty (real space) rg_real_error0.61 Å
I(0) (real space) i0_real2.1320e+07
I(0) uncertainty (real space) i0_real_error2.9750e+05
Rg (reciprocal space) rg_reciprocal20.95 Å
I(0) (reciprocal space) i0_reciprocal21320000.0000
Solution quality estimate total_estimate0.8276
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.3 Å
Skewness Skewness skewness0.528
Kurtosis Kurtosis kurtosis0.148
Angular range angular_range— – 0.3800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6661000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.614; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1d0va_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.39 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
Superfamily Superfamily superfamilyc.39.1 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
Family Family familyc.39.1.1 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)

CATH v4.4 (2 domains)

Domain ID domain_id1d0vA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1610 — 5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1
Homologous superfamily homologous superfamily10 — Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain
Domain ID domain_id1d0vA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10210 — Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain
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8. Citations (1)

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9. Files and Curves (10)