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

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Basic information

Entry
Database: PDB / ID: 3vmq
TitleCrystal structure of Staphylococcus aureus membrane-bound transglycosylase: Apoenzyme
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 / 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: 2.518 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,6533
Polymers60,6292
Non-polymers241
Water82946
1
A: Monofunctional glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3392
Polymers30,3141
Non-polymers241
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)66.683, 67.406, 152.810
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
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: 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: 2.5→30.079 Å / Num. obs: 23658 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.59 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: 2.518→30.079 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8011 / SU ML: 0.32 / σ(F): 0.02 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1104 5.12 %RANDOM
Rwork0.1999 ---
all0.2027 23609 --
obs0.2027 21577 89.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.035 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 294.13 Å2 / Biso mean: 80.3988 Å2 / Biso min: 20.21 Å2
Baniso -1Baniso -2Baniso -3
1--17.3752 Å2-0 Å20 Å2
2---16.5282 Å2-0 Å2
3---33.9033 Å2
Refinement stepCycle: LAST / Resolution: 2.518→30.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 1 46 3650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133669
X-RAY DIFFRACTIONf_angle_d0.8414945
X-RAY DIFFRACTIONf_chiral_restr0.063553
X-RAY DIFFRACTIONf_plane_restr0.002634
X-RAY DIFFRACTIONf_dihedral_angle_d18.2691331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5182-2.63270.31131220.23191993211572
2.6327-2.77140.24751250.2032278240381
2.7714-2.94490.24281160.20282368248484
2.9449-3.17210.23461460.19232525267190
3.1721-3.49090.2441430.17732785292898
3.4909-3.9950.23821530.17072784293798
3.995-5.02950.21911560.16792828298498
5.0295-30.08150.29721430.23712912305596
Refinement TLS params.Method: refined / Origin x: -24.3479 Å / Origin y: 1.2705 Å / Origin z: -5.0863 Å
111213212223313233
T0.3077 Å20.0498 Å20.0395 Å2-0.2284 Å20.0141 Å2--0.2515 Å2
L0.548 °2-0.3028 °20.0576 °2-0.4294 °2-0.4382 °2---0.1709 °2
S0.0945 Å °0.0603 Å °-0.0225 Å °-0.1531 Å °-0.0503 Å °0.1157 Å °-0.0665 Å °-0.0527 Å °-0.0044 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA41 - 269
2X-RAY DIFFRACTION1allB41 - 269
3X-RAY DIFFRACTION1allA1 - 4
4X-RAY DIFFRACTION1allA270 - 299
5X-RAY DIFFRACTION1allB5 - 6
6X-RAY DIFFRACTION1allB270 - 280

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