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

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Basic information

Entry
Database: PDB / ID: 3vmt
TitleCrystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with a Lipid II analog
ComponentsMonofunctional glycosyltransferase
KeywordsTRANSFERASE / Transmembrane / Glycosyltransferase / Bacterial cell wall synthesis / Membrane
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
Chem-LHI / Monofunctional glycosyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

Deposited unit
A: Monofunctional glycosyltransferase
B: Monofunctional glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5115
Polymers60,6292
Non-polymers1,8823
Water93752
1
A: Monofunctional glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1964
Polymers30,3141
Non-polymers1,8823
Water181
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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.493, 67.429, 152.186
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
#2: Chemical ChemComp-LHI / [(2R,3R,4R,5S,6R)-4-[(2R)-1-[[(2S)-1-[2-[2-[2-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]ethoxy]ethoxy]ethylamino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]oxy-3-acetamido-5-[(2S,3R,4R,5R,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-(hydroxymethyl)oxan-2-yl] [oxidanyl(3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenoxy)phosphoryl] hydrogen phosphate


Mass: 1833.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C93H155N7O23P2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND LHI IS THE ANALOG OF LIPIDII(LIIA).

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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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM MgCl2, 100mM HEPES, 25% PEG400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→29.26 Å / Num. obs: 30750 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 43.19 Å2
Reflection shellResolution: 2.2987→2.3808 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: 2.299→28.079 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7624 / SU ML: 0.27 / σ(F): 0.02 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 1437 5.09 %RANDOM
Rwork0.197 ---
obs0.1993 28206 90.4 %-
all-30698 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.778 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 265.53 Å2 / Biso mean: 87.1801 Å2 / Biso min: 29.31 Å2
Baniso -1Baniso -2Baniso -3
1--23.6442 Å2-0 Å20 Å2
2---14.1703 Å2-0 Å2
3---37.8145 Å2
Refinement stepCycle: LAST / Resolution: 2.299→28.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 45 52 3695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193711
X-RAY DIFFRACTIONf_angle_d0.9315007
X-RAY DIFFRACTIONf_chiral_restr0.071566
X-RAY DIFFRACTIONf_plane_restr0.008636
X-RAY DIFFRACTIONf_dihedral_angle_d24.2871399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2987-2.38080.33511110.25592189230075
2.3808-2.4760.26881250.23582382250782
2.476-2.58870.24071280.20952469259784
2.5887-2.7250.24511420.21042568271088
2.725-2.89560.28421480.20762736288494
2.8956-3.11890.27251480.21122780292895
3.1189-3.43230.25311540.20332887304198
3.4323-3.92780.20141590.17662943310298
3.9278-4.94420.22121670.16962922308998
4.9442-28.08090.23141550.20162893304892
Refinement TLS params.Method: refined / Origin x: -24.2765 Å / Origin y: -1.1594 Å / Origin z: 4.8341 Å
111213212223313233
T0.3713 Å2-0.034 Å2-0.033 Å2-0.3453 Å2-0.0056 Å2--0.4019 Å2
L0.3264 °20.2097 °2-0.0552 °2-0.1492 °2-0.274 °2---0.0799 °2
S0.0668 Å °0.0256 Å °0.0832 Å °0.076 Å °-0.0539 Å °0.0694 Å °-0.0179 Å °-0.0379 Å °0.0054 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA41 - 269
2X-RAY DIFFRACTION1allB41 - 269
3X-RAY DIFFRACTION1allA301
4X-RAY DIFFRACTION1allA302
5X-RAY DIFFRACTION1allA303
6X-RAY DIFFRACTION1allA401 - 441
7X-RAY DIFFRACTION1allB301 - 311

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