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- PDB-3hzs: S. aureus monofunctional glycosyltransferase (MtgA)in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3hzs
TitleS. aureus monofunctional glycosyltransferase (MtgA)in complex with moenomycin
ComponentsMonofunctional glycosyltransferase
KeywordsTRANSFERASE / transglycosylase / peptidoglycan / monofunctional / moenomycin / Cell membrane / Cell shape / Cell wall biogenesis/degradation / Glycosyltransferase / Membrane / Peptidoglycan synthesis / Transmembrane
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space / 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 / PHOSPHATE ION / Monofunctional glycosyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHeaslet, H. / Miller, A.A. / Shaw, B. / Mistry, A.
CitationJournal: 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
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 25, 2012Group: Other
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)25,9363
Polymers24,2611
Non-polymers1,6762
Water2,234124
1
A: Monofunctional glycosyltransferase
hetero molecules

A: Monofunctional glycosyltransferase
hetero molecules

A: Monofunctional glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8099
Polymers72,7833
Non-polymers5,0276
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area11400 Å2
ΔGint-38 kcal/mol
Surface area27250 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

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Components

#1: Protein Monofunctional glycosyltransferase / MGT / Peptidoglycan TGase


Mass: 24260.881 Da / Num. of mol.: 1 / Fragment: Staph. aureus monofunctional transglycosylase / Mutation: E100Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MW2 / Gene: mgt, MW1814 / Plasmid: pPW2-SA0933(2)-N3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)tolC-
References: UniProt: Q7A0I6, 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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Sa MtgA E100Q at 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 MtgA E100Q at 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 Mmoenomycin 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 22oC. Hexagonal plate crystals formed in 1 week., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / 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 / Num. unique all: 4606 / Rsym value: 0.381 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unpublished apo structure of MTGA

Resolution: 2.1→23.12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.49 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.178 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24379 963 5 %RANDOM
Rwork0.18917 ---
obs0.19183 18121 99.69 %-
all-45531 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.033 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å2-1.02 Å20 Å2
2---2.03 Å20 Å2
3---3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 105 124 1937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211891
X-RAY DIFFRACTIONr_angle_refined_deg1.81.9812566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96525.049103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69515312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.85159
X-RAY DIFFRACTIONr_chiral_restr0.1690.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021438
X-RAY DIFFRACTIONr_mcbond_it2.4011.51064
X-RAY DIFFRACTIONr_mcangle_it3.67521725
X-RAY DIFFRACTIONr_scbond_it5.6233827
X-RAY DIFFRACTIONr_scangle_it7.2794.5841
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 75 -
Rwork0.219 1321 -
obs--100 %

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