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- PDB-1d0v: CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIM... -

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Entry
Database: PDB / ID: 1d0v
TitleCRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH ITS REACTION PRODUCTS DETERMINED TO 1.9 A RESOLUTION
ComponentsNICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / DINUCLEOTIDE-BINDING MOTIF / PHOSPHORIBOSYLTRANSFERASE
Function / homology
Function and homology information


nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity / cobalamin biosynthetic process / nucleotide binding
Similarity search - Function
5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1 / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / Rossmann fold / Orthogonal Bundle ...5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1 / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINIC ACID / ALPHA-RIBAZOLE-5'-PHOSPHATE / Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsCheong, C.-G. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: 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
DepositionSep 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1273
Polymers36,6461
Non-polymers4812
Water2,846158
1
A: NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
hetero molecules

A: NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2546
Polymers73,2912
Non-polymers9634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6330 Å2
ΔGint-23 kcal/mol
Surface area21050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.1, 90.0, 47.6
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE


Mass: 36645.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria)
References: UniProt: Q05603, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
#2: Chemical ChemComp-RBZ / ALPHA-RIBAZOLE-5'-PHOSPHATE


Mass: 358.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N2O7P
#3: Chemical ChemComp-NIO / NICOTINIC ACID / Niacin


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#4: Water ChemComp-HOH / water / Water


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

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
21.3 Mammonium phosphate1reservoir
31 mMDMB1reservoir
44 %PEG4001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12771
22741
Diffraction source
SourceTypeIDWavelength
ROTATING ANODEENRAF-NONIUS11.5418
2
Detector
TypeIDDetectorDate
SIEMENS HI-STAR1AREA DETECTORJan 20, 1999
2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.88→1.98 Å / Redundancy: 1.3 % / % possible all: 65
Reflection shell
*PLUS
% possible obs: 65 %

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Processing

Software
NameClassification
FRAMBOdata collection
XDSdata reduction
SOLVEphasing
TNTrefinement
XDSdata scaling
RefinementResolution: 1.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.249 --10 % OF DATA WERE OMITTED RANDOMLY
Rwork0.16 ---
all0.163 25069 --
obs-21894 87.3 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 33 158 2609
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.83
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / Rfactor all: 0.163 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.83
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.7

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