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- PDB-4y7t: Structural analysis of MurU -

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Basic information

Entry
Database: PDB / ID: 4y7t
TitleStructural analysis of MurU
ComponentsNucleotidyl transferaseNucleotidyltransferase
KeywordsTRANSFERASE / Nucleotidyltransferase family protein / uridyltransferase / Rossman fold
Function / homology
Function and homology information


N-acetylmuramic acid metabolic process / N-acetyl-alpha-D-muramate 1-phosphate uridylyltransferase / uridylyltransferase activity / peptidoglycan turnover / carbohydrate derivative binding / UTP binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process ...N-acetylmuramic acid metabolic process / N-acetyl-alpha-D-muramate 1-phosphate uridylyltransferase / uridylyltransferase activity / peptidoglycan turnover / carbohydrate derivative binding / UTP binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / response to antibiotic / magnesium ion binding
Similarity search - Function
Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / N-acetylmuramate alpha-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsRenner-Schneck, M.G. / Stehle, T.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of the N-Acetylmuramic Acid alpha-1-Phosphate (MurNAc-alpha 1-P) Uridylyltransferase MurU, a Minimal Sugar Nucleotidyltransferase and Potential Drug Target Enzyme in Gram-negative Pathogens.
Authors: Renner-Schneck, M. / Hinderberger, I. / Gisin, J. / Exner, T. / Mayer, C. / Stehle, T.
History
DepositionFeb 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleotidyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4827
Polymers24,9131
Non-polymers5686
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-52 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.610, 72.610, 158.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Detailsbiological unit is the same as asym.

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Components

#1: Protein Nucleotidyl transferase / Nucleotidyltransferase / MurU


Mass: 24913.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: BIRD-1 / Gene: PPUBIRD1_0444 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / References: UniProt: E4RE40, UniProt: Q88QT2*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: (NH4)2SO4, MES

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Data collection

DiffractionMean temperature: 93.2 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 23700 / % possible obs: 99.9 % / Redundancy: 9.8 % / Net I/σ(I): 13.31

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.8→40.446 Å / FOM work R set: 0.7264 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 32.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 1185 5 %Random selection
Rwork0.2114 22503 --
obs0.2132 23688 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.65 Å2 / Biso mean: 47.26 Å2 / Biso min: 24.73 Å2
Refinement stepCycle: final / Resolution: 1.8→40.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 62 80 1755
Biso mean--64.66 49.96 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151764
X-RAY DIFFRACTIONf_angle_d1.5262405
X-RAY DIFFRACTIONf_chiral_restr0.066268
X-RAY DIFFRACTIONf_plane_restr0.008307
X-RAY DIFFRACTIONf_dihedral_angle_d15.15652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8820.36491430.3192717286099
1.882-1.98120.35351450.296927562901100
1.9812-2.10530.38091450.318427492894100
2.1053-2.26780.3071460.25127732919100
2.2678-2.4960.25351460.232427842930100
2.496-2.85710.28381480.249428132961100
2.8571-3.59930.26441510.216528543005100
3.5993-40.45650.19161610.168430573218100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.0413-0.99940.29652.8321-0.47162.39030.09040.0342-0.1942-0.0477-0.00470.3363-0.0019-0.2403-0.09170.2430.025-0.03260.38510.02670.31499.348531.078-0.4944
24.26772.11490.76152.8501-0.07283.38760.1494-0.0067-0.0314-0.0812-0.1141-0.04790.2111-0.1917-0.05310.25130.0206-0.02120.320.01890.330119.395627.50479.1526
36.02151.43880.14954.9133-1.27873.22230.2668-0.64610.24670.5948-0.2518-0.1869-0.26020.1066-0.04410.3225-0.0175-0.02060.39820.00550.246926.754131.825917.1293
43.28-3.13283.50034.7379-0.98316.9830.3683-1.1501-0.15810.3627-0.21380.60680.1949-1.1983-0.03350.3979-0.1044-0.02180.7030.03890.387616.143427.051622.6646
54.0964-0.61661.3342.63730.61232.5693-0.02850.4330.6273-0.1841-0.2399-0.2423-0.69940.35180.23320.3706-0.0335-0.00660.38610.08990.332324.312740.45352.9413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:79)A1 - 79
2X-RAY DIFFRACTION2(chain A and resid 80:133)A80 - 133
3X-RAY DIFFRACTION3(chain A and resid 139:171)A139 - 171
4X-RAY DIFFRACTION4(chain A and resid 172:191)A172 - 191
5X-RAY DIFFRACTION5(chain A and resid 192:224)A192 - 224

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