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- PDB-4y7v: Structural analysis of MurU -

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Basic information

Entry
Database: PDB / ID: 4y7v
TitleStructural analysis of MurU
ComponentsNucleotidyl transferase
KeywordsTRANSFERASE / Nucleotidyltransferase family protein / uridyltransferase / Rossman fold / MurNAc-1P
Function / homology
Function and homology information


N-acetyl-alpha-D-muramate 1-phosphate uridylyltransferase / N-acetylmuramic acid metabolic process / uridylyltransferase activity / peptidoglycan turnover / carbohydrate derivative binding / UTP binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / 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
IMIDODIPHOSPHORIC ACID / Chem-491 / : / 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
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,6525
Polymers24,9131
Non-polymers7384
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-20 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.350, 72.350, 162.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

Detailsbiological unit is the same as asym.

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Nucleotidyl transferase / MurU


Mass: 24913.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain BIRD-1) (bacteria)
Strain: BIRD-1 / Gene: PPUBIRD1_0444 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / References: UniProt: E4RE40, UniProt: Q88QT2*PLUS
#4: Sugar ChemComp-491 / 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / 2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / N-acetyl-3-O-[(1R)-1-carboxyethyl]-1-O-phosphono-alpha-D-glucosamine / 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-D-glucose / 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 373.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20NO11P

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Non-polymers , 4 types, 70 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-2PN / IMIDODIPHOSPHORIC ACID


Mass: 176.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5NO6P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: (NH4)2SO4, MES

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Data collection

DiffractionMean temperature: 93.2 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 18, 2013
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: 24133 / % possible obs: 99.9 % / Redundancy: 20 % / Net I/σ(I): 27.7
Reflection shellResolution: 1.8→1.85 Å / Mean I/σ(I) obs: 0.91 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.8→49.615 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1207 5 %Random selection
Rwork0.2149 22925 --
obs0.2169 24132 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.35 Å2 / Biso mean: 52.21 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.8→49.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 88 67 1751
Biso mean--60.3 56.86 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071743
X-RAY DIFFRACTIONf_angle_d1.0742380
X-RAY DIFFRACTIONf_chiral_restr0.042269
X-RAY DIFFRACTIONf_plane_restr0.005303
X-RAY DIFFRACTIONf_dihedral_angle_d14.949634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.87220.35991300.347324812611
1.8722-1.95740.3611320.337124962628
1.9574-2.06060.32761310.277224942625
2.0606-2.18970.30391310.261924882619
2.1897-2.35880.30241320.241724992631
2.3588-2.59610.30431330.24525392672
2.5961-2.97170.28341350.243325522687
2.9717-3.74390.22721360.204525972733
3.7439-49.63360.22481470.182627792926

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