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- PDB-3vmr: Crystal structure of Staphylococcus aureus membrane-bound transgl... -

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Basic information

Entry
Database: PDB / ID: 3vmr
TitleCrystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with moenomycin
ComponentsMonofunctional glycosyltransferase
KeywordsTRANSFERASE / Transmembrane / Glycosyltransferase / Bacterial cell wall synthesis / Membrane
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
MOENOMYCIN / Monofunctional glycosyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.688 Å
AuthorsHuang, C.Y. / Shih, H.W. / Lin, L.Y. / Tien, Y.W. / Cheng, T.J.R. / Cheng, W.C. / Wong, C.H. / Ma, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structure of Staphylococcus aureus transglycosylase in complex with a lipid II analog and elucidation of peptidoglycan synthesis mechanism
Authors: Huang, C.Y. / Shih, H.W. / Lin, L.Y. / Tien, Y.W. / Cheng, T.J.R. / Cheng, W.C. / Wong, C.H. / Ma, C.
History
DepositionDec 15, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Monofunctional glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8952
Polymers30,3141
Non-polymers1,5811
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.423, 52.852, 54.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Monofunctional glycosyltransferase / MGT / Peptidoglycan TGase


Mass: 30314.369 Da / Num. of mol.: 1 / Fragment: residues 28-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: mgt / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: Q99T05, Transferases; Glycosyltransferases
#2: Chemical ChemComp-M0E / MOENOMYCIN / MOENOMYCIN


Mass: 1580.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H106N5O34P / Comment: antibiotic*YM

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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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25mM Na malonate, 11.5% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.68→28.598 Å / Num. obs: 4460 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 3.6879→3.83 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HZS, 3FWM, 3FWL

3hzs

3fwm
PDB Unreleased entry

3fwl


Resolution: 3.688→28.598 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.577 / SU ML: 0.67 / σ(F): 0.06 / Phase error: 43.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3092 190 4.72 %RANDOM
Rwork0.3033 ---
obs0.3036 4028 91.52 %-
all-4344 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 126.995 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso max: 370.12 Å2 / Biso mean: 176.1767 Å2 / Biso min: 90.46 Å2
Baniso -1Baniso -2Baniso -3
1--52.5432 Å20 Å2-0 Å2
2--77.9079 Å20 Å2
3----25.3647 Å2
Refinement stepCycle: LAST / Resolution: 3.688→28.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 84 0 1938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051975
X-RAY DIFFRACTIONf_angle_d1.1342676
X-RAY DIFFRACTIONf_chiral_restr0.083311
X-RAY DIFFRACTIONf_plane_restr0.007334
X-RAY DIFFRACTIONf_dihedral_angle_d34.365809
LS refinement shellResolution: 3.6879→3.83 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.3092 190 -
Rwork0.3033 3838 -
all-4028 -
obs--92 %
Refinement TLS params.Method: refined / Origin x: 22.1429 Å / Origin y: 5.9705 Å / Origin z: 12.4435 Å
111213212223313233
T1.0066 Å20.0218 Å2-0.1029 Å2-0.86 Å2-0.0137 Å2--0.8807 Å2
L3.3627 °21.0033 °22.1422 °2-3.7644 °22.8131 °2--2.7408 °2
S0.1003 Å °-0.3785 Å °-0.0903 Å °0.1986 Å °0.0735 Å °-0.9547 Å °0.2933 Å °0.0753 Å °-0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA41 - 269
2X-RAY DIFFRACTION1allA901

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