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- PDB-3s2u: Crystal structure of the Pseudomonas aeruginosa MurG:UDP-GlcNAc s... -

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Basic information

Entry
Database: PDB / ID: 3s2u
TitleCrystal structure of the Pseudomonas aeruginosa MurG:UDP-GlcNAc substrate complex
ComponentsUDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
KeywordsTRANSFERASE / N-acetylglucosaminyl transferase
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 / lipid glycosylation / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / 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
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.23 Å
AuthorsBrown, K. / Vial, S.C.M. / Dedi, N. / Westcott, J. / Scally, S. / Bugg, T.D.H. / Charlton, P.A. / Cheetham, G.M.T.
CitationJournal: Protein Pept.Lett. / Year: 2013
Title: Crystal Structure of the Pseudomonas aeruginosa MurG: UDP-GlcNAc Substrate Complex.
Authors: Brown, K. / Vial, S.C. / Dedi, N. / Westcott, J. / Scally, S. / Bugg, T.D. / Charlton, P.A. / Cheetham, G.M.
History
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Feb 28, 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

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5262
Polymers38,9191
Non-polymers6071
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.930, 49.930, 278.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase / Undecaprenyl-PP-MurNAc-pentapeptide-UDPGlcNAc GlcNAc transferase


Mass: 38919.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: murG, PA4412
References: UniProt: Q9HW01, undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 18% PEG3350, 0.1M HEPES pH 7.0 and 10mM DTT, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 15355 / % possible obs: 84.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameClassification
DNAdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 2.23→20 Å / Cor.coef. Fo:Fc: 0.8952 / Cor.coef. Fo:Fc free: 0.8458 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.417 / SU Rfree Blow DPI: 0.278 / SU Rfree Cruickshank DPI: 0.271
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 1018 6.64 %RANDOM
Rwork0.2094 ---
obs0.2139 15329 83.81 %-
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.5382 Å20 Å20 Å2
2--1.5382 Å20 Å2
3----3.0764 Å2
Refinement stepCycle: LAST / Resolution: 2.23→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 39 115 2613
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092546HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.193480HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d840SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes377HARMONIC5
X-RAY DIFFRACTIONt_it2546HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion18.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion330SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2911SEMIHARMONIC4
LS refinement shellResolution: 2.23→2.38 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2769 160 7.34 %
Rwork0.1994 2021 -
all0.2049 2181 -
obs--83.81 %
Refinement TLS params.Method: refined / Origin x: 10.5945 Å / Origin y: -19.4419 Å / Origin z: -19.1213 Å
111213212223313233
T0.304 Å2-0.0778 Å2-0.0659 Å2--0.294 Å20.0244 Å2---0.2157 Å2
L0.7215 °2-0.5682 °2-0.501 °2-1.9163 °20.7665 °2--0.982 °2
S-0.0199 Å °-0.0795 Å °0.016 Å °0.0695 Å °0.0457 Å °0.0856 Å °-0.0284 Å °0.059 Å °-0.0258 Å °
Refinement TLS groupSelection details: { A|* }

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