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- PDB-1f0k: THE 1.9 ANGSTROM CRYSTAL STRUCTURE OF E. COLI MURG -

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Basic information

Entry
Database: PDB / ID: 1f0k
TitleTHE 1.9 ANGSTROM CRYSTAL STRUCTURE OF E. COLI MURG
ComponentsUDP-N-ACETYLGLUCOSAMINE-N-ACETYLMURAMYL-(PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE TRANSFERASE
KeywordsTRANSFERASE / Rossmann fold
Function / homology
Function and homology information


undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase / undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase activity / UDP-N-acetyl-D-glucosamine:N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol 4-beta-N-acetylglucosaminlytransferase activity / : / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell division / plasma membrane
Similarity search - Function
N-acetylglucosaminyltransferase, MurG / Glycosyl transferase, family 28, C-terminal / Glycosyltransferase family 28, N-terminal domain / Glycosyltransferase family 28 N-terminal domain / Glycosyltransferase family 28 C-terminal domain / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsHa, S. / Walker, D. / Shi, Y. / Walker, S.
CitationJournal: Protein Sci. / Year: 2000
Title: The 1.9 A crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis.
Authors: Ha, S. / Walker, D. / Shi, Y. / Walker, S.
History
DepositionMay 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE-N-ACETYLMURAMYL-(PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE TRANSFERASE
B: UDP-N-ACETYLGLUCOSAMINE-N-ACETYLMURAMYL-(PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2183
Polymers78,1222
Non-polymers961
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.613, 66.356, 67.902
Angle α, β, γ (deg.)64.29, 83.52, 65.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE-N-ACETYLMURAMYL-(PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE TRANSFERASE / MURG


Mass: 39060.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21B / Production host: Escherichia coli (E. coli)
References: UniProt: P17443, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: NaMES, ammonium sulfate, TritonX-100, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7.9
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
3150 mM1dropNaCl
450 mMEDTA1drop
50.1 MNaMES1reservoir
60.96 Mammonium sulfate1reservoir
70.4 %Triton-X-1001reservoir
810 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.0092
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0092 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 65567 / Num. obs: 65567 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 41.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.79 % / Rmerge(I) obs: 0.187 / Num. unique all: 6450 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 288150
Reflection shell
*PLUS
% possible obs: 96.4 % / Mean I/σ(I) obs: 7

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→40 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 6224 -RANDOM
Rwork0.22 ---
all-65277 --
obs-61989 91 %-
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5278 0 5 296 5579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.295
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS

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