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- PDB-5zzk: A Con Artist: Phenylphenoxybenzamide is not a Glycosyltransferase... -

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Basic information

Entry
Database: PDB / ID: 5zzk
TitleA Con Artist: Phenylphenoxybenzamide is not a Glycosyltransferase Inhibitor
ComponentsMonofunctional glycosyltransferase
KeywordsSUGAR BINDING PROTEIN / glycosyltransferase membrane associated enzyme lipid II polymerization PBP class A
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / plasma membrane
Similarity search - Function
Monofunctional glycosyl transferase / Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Monofunctional glycosyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWybenga, G.G.
CitationJournal: Biorxiv / Year: 2018
Title: A Con Artist: Phenylphenoxybenzamide is not a Glycosyltransferase Inhibitor
Authors: Wybenga, G.G. / Wu, W.S.
History
DepositionJun 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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: Monofunctional glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)28,4251
Polymers28,4251
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: based on the packing of the monoglycosyltransferase molecules in the protein crystal
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9840 Å2
Unit cell
Length a, b, c (Å)153.880, 39.640, 55.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Monofunctional glycosyltransferase / MGT / Peptidoglycan TGase


Mass: 28425.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: mgt, SAV1874 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99T05, peptidoglycan glycosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3 Å3/Da / Density % sol: 63.87 %
Crystal growTemperature: 278.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM MgCl2, 100 mM Na HEPES pH 8, and 16 % wt/vol PEG400 (Sigma)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.97622 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.64→30 Å / Num. obs: 8774 / % possible obs: 51 % / Redundancy: 2.1 % / Net I/σ(I): 9.1
Reflection shellResolution: 2.64→2.71 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.5 / % possible all: 51

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VMQ

3vmq


Resolution: 2.64→30 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.702 / SU B: 24.618 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.572 / ESU R Free: 0.4
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3273 465 5.3 %RANDOM
Rwork0.2451 ---
obs0.2493 8281 82.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.64 Å2 / Biso mean: 39.947 Å2 / Biso min: 18.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å2-0 Å20 Å2
2--2.3 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 2.64→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 0 6 1503
Biso mean---23.53 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191525
X-RAY DIFFRACTIONr_bond_other_d0.0020.021337
X-RAY DIFFRACTIONr_angle_refined_deg2.1421.9192057
X-RAY DIFFRACTIONr_angle_other_deg1.23833113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8725179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31425.41285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.15415270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.46155
X-RAY DIFFRACTIONr_chiral_restr0.130.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021695
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02314
LS refinement shellResolution: 2.641→2.709 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 3 -
Rwork0.246 138 -
all-141 -
obs--19.42 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.43060.13520.57490.37190.29181.7822-0.03620.1263-0.2454-0.08460.0396-0.36990.28240.6436-0.00340.40120.0930.12590.25060.07910.4336-19.59915-13.48
25.9050.77197.84941.73460.255410.8503-0.13640.0662-0.19290.1424-0.0069-0.7596-0.13370.22110.14330.3080.23320.11690.35190.10220.469-21.14513.258-9.414
31.47770.5344-0.16662.4628-0.3122.5651-0.05760.16250.0293-0.0218-0.0438-0.15260.00690.11510.10130.21030.00540.01120.04360.01270.0699-33.15422.956-12.487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 108
2X-RAY DIFFRACTION2A133 - 144
3X-RAY DIFFRACTION3A155 - 268

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