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- PDB-4kqg: Crystal structure of CobT E174A complexed with DMB -

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Basic information

Entry
Database: PDB / ID: 4kqg
TitleCrystal structure of CobT E174A complexed with DMB
ComponentsNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
KeywordsTRANSFERASE
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
5,6-DIMETHYLBENZIMIDAZOLE / PHOSPHATE ION / Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsChan, C.H. / Newmister, S.A. / Taylor, K.C. / Claas, K.R. / Rayment, I. / Escalante-Semerena, J.C.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Dissecting cobamide diversity through structural and functional analyses of the base-activating CobT enzyme of Salmonella enterica.
Authors: Chan, C.H. / Newmister, S.A. / Talyor, K. / Claas, K.R. / Rayment, I. / Escalante-Semerena, J.C.
History
DepositionMay 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)36,8914
Polymers36,5881
Non-polymers3033
Water5,278293
1
A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules

A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7828
Polymers73,1752
Non-polymers6066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area5840 Å2
ΔGint-35 kcal/mol
Surface area21490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.907, 89.033, 46.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase / NN:DBI PRT / N(1)-alpha-phosphoribosyltransferase


Mass: 36587.531 Da / Num. of mol.: 1 / Mutation: E174A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: cobT, STM2016 / Plasmid: pCOBT42 / Production host: Escherichia coli (E. coli) / Strain (production host): JE2017
References: UniProt: Q05603, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-DMD / 5,6-DIMETHYLBENZIMIDAZOLE


Mass: 146.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 10% MEPEG 5000, 0.1 M MES, 0.2 M ammonium sulfate, 5% glycerol, pH 6.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 13, 2012 / Details: Montel
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 24307 / Num. obs: 24307 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.8 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata reduction
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
PROTEUM PLUSPLUSdata collection
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.155 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 1231 5.1 %RANDOM
Rwork0.1698 ---
all0.1726 24171 --
obs0.1726 24171 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.82 Å2 / Biso mean: 8.2686 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2---0.29 Å2-0 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 20 293 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192526
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.9873448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18224.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17615378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6411513
X-RAY DIFFRACTIONr_chiral_restr0.1290.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211886
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 81 -
Rwork0.244 1563 -
all-1644 -
obs--93.3 %

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