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

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Basic information

Entry
Database: PDB / ID: 3vms
TitleCrystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with NBD-Lipid II
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
Monofunctional glycosyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.202 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monofunctional glycosyltransferase
B: Monofunctional glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)60,6292
Polymers60,6292
Non-polymers00
Water00
1
A: Monofunctional glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)30,3141
Polymers30,3141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monofunctional glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)30,3141
Polymers30,3141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.878, 67.159, 140.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Monofunctional glycosyltransferase / MGT / Peptidoglycan TGase


Mass: 30314.369 Da / Num. of mol.: 2 / 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

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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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM MgCl2, 100mM HEPES, 25% PEG400, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 10888 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 83.62 Å2

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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: 3.202→29.934 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6679 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 37.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3298 522 4.82 %RANDOM
Rwork0.2615 ---
all0.2649 10845 --
obs0.2649 10838 99.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.054 Å2 / ksol: 0.246 e/Å3
Displacement parametersBiso max: 407.54 Å2 / Biso mean: 132.1718 Å2 / Biso min: 34.93 Å2
Baniso -1Baniso -2Baniso -3
1--31.1833 Å2-0 Å20 Å2
2---0.8404 Å2-0 Å2
3---32.0236 Å2
Refinement stepCycle: LAST / Resolution: 3.202→29.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 0 0 3565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063629
X-RAY DIFFRACTIONf_angle_d1.0164892
X-RAY DIFFRACTIONf_chiral_restr0.071544
X-RAY DIFFRACTIONf_plane_restr0.003629
X-RAY DIFFRACTIONf_dihedral_angle_d20.2631310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2017-3.52350.35531380.27212483262198
3.5235-4.03230.32261280.222725592687100
4.0323-5.07620.27931240.19125852709100
5.0762-29.93510.33991320.29992689282199
Refinement TLS params.Method: refined / Origin x: 24.6065 Å / Origin y: -34.1327 Å / Origin z: -12.2568 Å
111213212223313233
T0.3202 Å2-0.1704 Å20.1054 Å2-0.421 Å20.0194 Å2--0.3513 Å2
L2.4446 °2-0.4489 °2-0.849 °2--0.1962 °20.0078 °2--3.3835 °2
S-0.3378 Å °0.1434 Å °-0.0277 Å °0.3363 Å °0.3681 Å °-0.2182 Å °0.4755 Å °0.1279 Å °0.0445 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA43 - 269
2X-RAY DIFFRACTION1allB45 - 269

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