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- PDB-6ftb: Staphylococcus aureus monofunctional glycosyltransferase in compl... -

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Basic information

Entry
Database: PDB / ID: 6ftb
TitleStaphylococcus aureus monofunctional glycosyltransferase in complex with moenomycin
ComponentsMonofunctional glycosyltransferase
KeywordsTRANSFERASE / TRANSGLYCOSYLASE / PEPTIDOGLYCAN / MONOFUNCTIONAL / MOENOMYCIN / INHIBITOR / MEMBRANE / CELL SHAPE / CELL WALL BIOSYNTHESIS / GLYCOSYLTRANSFERASE / PEPTIDOGLYCAN SYNTHESIS / ANTIBIOTICS
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / 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
(2R)-2,3-dihydroxypropyl dodecanoate / MOENOMYCIN / PHOSPHATE ION / Monofunctional glycosyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus MW2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPunekar, A.S. / Dowson, C.J. / Roper, D.I.
Citation
Journal: Cell Surf / Year: 2018
Title: The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization.
Authors: Punekar, A.S. / Samsudin, F. / Lloyd, A.J. / Dowson, C.G. / Scott, D.J. / Khalid, S. / Roper, D.I.
#1: Journal: J Struct Biol. / Year: 2009
Title: Characterization of the active site of S. aureus monofunctional glycosyltransferase (Mtg) by site-directed mutation and structural analysis of the protein complexed with moenomycin.
Authors: Heaslet, H. / Shaw, B. / Mistry, A. / Miller, A.A.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monofunctional glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,09315
Polymers24,3901
Non-polymers5,70314
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint18 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.422, 114.422, 128.844
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-301-

M0E

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Monofunctional glycosyltransferase / MGT / Peptidoglycan TGase


Mass: 24389.998 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus MW2 (bacteria) / Gene: mgt, MW1814 / Plasmid: PPW2-SA0933(2)-N3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TolC-
References: UniProt: Q7A0I6, peptidoglycan glycosyltransferase

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-M0E / MOENOMYCIN / MOENOMYCIN / Moenomycin family antibiotics


Mass: 1580.567 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C69H106N5O34P / Comment: antibiotic*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-1QW / (2R)-2,3-dihydroxypropyl dodecanoate / 1-Lauroyl-rac-glycerol


Mass: 274.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.35 Å3/Da / Density % sol: 63.23 %
Description: HEXAGONAL PLATE CRYSTALS APPEARED WITHIN 1 WEEK.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: SA MGT E100Q (10 MG/ML) WAS MIXED WITH 1MM MOENOMYCIN AND 1MM MNCL2 AND INCUBATED ON ICE FOR ~3 HOURS. PRECIPITATED MATERIAL WAS REMOVED BY CENTRIFUGATION AT 16, 000XG FOR 5 MINUTES. THE ...Details: SA MGT E100Q (10 MG/ML) WAS MIXED WITH 1MM MOENOMYCIN AND 1MM MNCL2 AND INCUBATED ON ICE FOR ~3 HOURS. PRECIPITATED MATERIAL WAS REMOVED BY CENTRIFUGATION AT 16, 000XG FOR 5 MINUTES. THE MOENOMYCIN COMPLEX WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION, MIXING THE PROTEIN 1:1 WITH A RESERVOIR SOLUTION CONTAINING 0.1M NA ACETATE PH 4.6, 0.2M NACL, 30% MPD AT 295 K.
PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 12, 2007 / Details: RIGAKU VARIMAX HF OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→23.12 Å / Num. obs: 45531 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 37.46 Å2 / Rsym value: 0.173 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.381 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HZS

3hzs


Resolution: 2.1→23.12 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.193 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.237 963 5.05 %RANDOM
Rwork0.197 ---
obs0.199 19082 99.8 %-
Displacement parametersBiso mean: 42.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.9141 Å20 Å20 Å2
2--0.9141 Å20 Å2
3----1.8282 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→23.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 216 158 2087
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011979HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.062676HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d754SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes290HARMONIC5
X-RAY DIFFRACTIONt_it1979HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion19.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion266SEMIHARMONIC5
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_contact2648SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.268 142 5.15 %
Rwork0.221 2616 -
all0.223 2758 -
obs--100 %

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