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- PDB-1l5m: Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)-2... -

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Basic information

Entry
Database: PDB / ID: 1l5m
TitleCrystal Structure of CobT complexed with N7-(5'-phosphoribosyl)-2-aminopurine and nicotinate
ComponentsNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
KeywordsTRANSFERASE / CobT / cobalamin synthetic enzyme / phosphoribosyltransferase / 5 / 6-dimethylbenzimidazole / nicotinate mononucleotide
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 / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / 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 / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / 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
Chem-7RA / NICOTINIC ACID / Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsCheong, C.-G. / Escalante-Semerena, J. / Rayment, I.
CitationJournal: Biochemistry / Year: 2002
Title: Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes.
Authors: Cheong, C.G. / Escalante-Semerena, J.C. / Rayment, I.
History
DepositionMar 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1463
Polymers36,6761
Non-polymers4702
Water2,504139
1
A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules

A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2926
Polymers73,3512
Non-polymers9414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area5880 Å2
ΔGint-27 kcal/mol
Surface area21230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.740, 90.170, 47.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
DetailsThe biological assembly is a dimer generated from one monomer in asymmetric unit by crystallographic two-fold axis

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Components

#1: Protein Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase / E.C.2.4.2.21 / CobT / NN:DBI PRT / N1-alpha-phosphoribosyltransferase / Nicotinate Mononucleotide:5 / 6- ...CobT / NN:DBI PRT / N1-alpha-phosphoribosyltransferase / Nicotinate Mononucleotide:5 / 6-Dimethylbenzimidazole Phosphoribosyltransferase


Mass: 36675.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: cobt / Plasmid: pT7-5 / Production host: Salmonella enterica (bacteria) / Strain (production host): JE2461
References: UniProt: Q05603, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
#2: Chemical ChemComp-7RA / 7-ALPHA-D-RIBOFURANOSYL-2-AMINOPURINE-5'-PHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Chemical ChemComp-NIO / NICOTINIC ACID


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


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Details: double focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. all: 19462 / Num. obs: 19462 / % possible obs: 88.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.06 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 2.6 / % possible all: 66.8

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Processing

Software
NameClassification
XDSdata reduction
CNSrefinement
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1D0S

1d0s


Resolution: 2→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 942 4.8 %random
Rwork0.168 ---
all-19462 --
obs-19462 --
Refinement stepCycle: LAST / Resolution: 2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 32 139 2560
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.37

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