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- PDB-4kqj: Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol... -

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Basic information

Entry
Database: PDB / ID: 4kqj
TitleCrystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN
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
NICOTINATE MONONUCLEOTIDE / P-CRESOL / Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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

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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)37,2824
Polymers36,7431
Non-polymers5393
Water3,135174
1
A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules

A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5648
Polymers73,4862
Non-polymers1,0796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6550 Å2
ΔGint-86 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.807, 89.154, 46.944
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsthe biological unit is a dimer

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Components

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


Mass: 36742.766 Da / Num. of mol.: 1 / Mutation: S80Y, Q88M, L175M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: cobT, STM2016 / Plasmid: pCOBT184 / Production host: Escherichia coli (E. coli) / Strain (production host): JE13607
References: UniProt: Q05603, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
#2: Chemical ChemComp-NCN / NICOTINATE MONONUCLEOTIDE / NAMN


Mass: 335.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO9P
#3: Chemical ChemComp-PCR / P-CRESOL


Mass: 108.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9
Details: 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

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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: Oct 9, 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: 22398 / Num. obs: 22398 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.1 / % possible all: 93.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 3.477 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 1125 5.1 %RANDOM
Rwork0.1816 ---
all0.1836 22112 --
obs0.1836 22112 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.2 Å2 / Biso mean: 9.187 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0 Å2
2--0.32 Å2-0 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2453 0 35 174 2662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192554
X-RAY DIFFRACTIONr_bond_other_d0.0010.022493
X-RAY DIFFRACTIONr_angle_refined_deg2.1091.9953492
X-RAY DIFFRACTIONr_angle_other_deg1.0383.0015717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22524.45883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23715383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9231513
X-RAY DIFFRACTIONr_chiral_restr0.3310.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02516
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 78 -
Rwork0.204 1252 -
all-1330 -
obs--81.3 %

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