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- PDB-2olv: Structural Insight Into the Transglycosylation Step Of Bacterial ... -

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Basic information

Entry
Database: PDB / ID: 2olv
TitleStructural Insight Into the Transglycosylation Step Of Bacterial Cell Wall Biosynthesis : Donor Ligand Complex
ComponentsPenicillin-binding protein 2
KeywordsTRANSFERASE / transpeptidase fold / glycosyltransferase family 51 / lysozyme fold
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / membrane
Similarity search - Function
Penicillin-binding protein 2a (Domain 2) - #20 / Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase ...Penicillin-binding protein 2a (Domain 2) - #20 / Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MOENOMYCIN / : / peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLovering, A.L. / De Castro, L. / Lim, D. / Strynadka, N.C.J.
CitationJournal: Science / Year: 2007
Title: Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis.
Authors: Lovering, A.L. / de Castro, L.H. / Lim, D. / Strynadka, N.C.
History
DepositionJan 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 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 / struct_conn / struct_ncs_dom_lim / 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_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Residue 59 is an initiating methionine and a modified residue

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 2
B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,4414
Polymers149,2802
Non-polymers3,1612
Water00
1
A: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2212
Polymers74,6401
Non-polymers1,5811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2212
Polymers74,6401
Non-polymers1,5811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.565, 212.211, 91.635
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEU2AA67 - 2809 - 222
21ALAALALEULEU2BB67 - 2809 - 222
32ASNASNHISHIS4AA300 - 692242 - 634
42ASNASNHISHIS4BB300 - 692242 - 634

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Components

#1: Protein Penicillin-binding protein 2


Mass: 74640.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: pbp2 / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta lambda DE3
References: UniProt: Q2YY56, UniProt: Q9R744*PLUS, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-M0E / MOENOMYCIN / MOENOMYCIN


Mass: 1580.567 Da / Num. of mol.: 2 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM Na citrate, 0.1M NaCl, 0.1M MgCl2, 12% PEG 4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2006
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→44.151 Å / Num. obs: 39086 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 6.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 1.2 / Num. measured all: 27580 / Num. unique all: 5661 / Rsym value: 0.565 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→44.15 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / SU B: 44.767 / SU ML: 0.384 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1955 5 %RANDOM
Rwork0.231 ---
all0.231 ---
obs0.234 39038 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.621 Å2
Baniso -1Baniso -2Baniso -3
1--6.1 Å20 Å20 Å2
2---5.48 Å20 Å2
3---11.58 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9710 0 168 0 9878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210098
X-RAY DIFFRACTIONr_bond_other_d0.0030.026716
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9713679
X-RAY DIFFRACTIONr_angle_other_deg0.8833.00316312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65651231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09525.431499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.534151687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2211534
X-RAY DIFFRACTIONr_chiral_restr0.0730.21467
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021965
X-RAY DIFFRACTIONr_nbd_refined0.2290.22535
X-RAY DIFFRACTIONr_nbd_other0.1840.26918
X-RAY DIFFRACTIONr_nbtor_refined0.1880.24964
X-RAY DIFFRACTIONr_nbtor_other0.0880.25356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.25
X-RAY DIFFRACTIONr_mcbond_it0.6481.56330
X-RAY DIFFRACTIONr_mcbond_other0.0951.52520
X-RAY DIFFRACTIONr_mcangle_it1.00329810
X-RAY DIFFRACTIONr_scbond_it1.02334405
X-RAY DIFFRACTIONr_scangle_it1.5274.53869
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1213TIGHT POSITIONAL0.030.05
6809MEDIUM POSITIONAL0.340.5
1213TIGHT THERMAL0.040.5
6809MEDIUM THERMAL0.372
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 146 -
Rwork0.428 2719 -
obs-2865 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.29070.8293-3.42615.3719-0.98462.1678-1.0105-0.71650.9108-0.74850.5437-0.62950.57060.32110.4668-0.1548-0.1415-0.1342-0.38740.09920.3965-17.349187.4747-5.1398
210.5515-6.00693.93034.09072.182230.5792-0.5112.38230.324-0.6301-0.460.6078-0.9464-1.22370.971-0.0111-0.1761-0.035-0.04570.1653-0.0367-35.985588.4867-16.9055
32.5568-0.9322-0.68621.79180.17920.7346-0.3467-0.3296-0.74120.10160.14880.183-0.08630.03670.1979-0.1051-0.01820.1295-0.04350.0607-0.0366-20.261433.1603-4.027
410.59571.72032.75778.88141.11364.0815-0.8547-0.43160.0233-0.89540.34341.2655-0.5393-0.2860.5113-0.2903-0.1527-0.1181-0.6267-0.03970.1474-22.631418.051646.8835
55.44981.1159-3.76265.082310.186627.3324-0.75542.7023-0.3524-0.29720.31730.466-0.34481.96030.4382-0.0146-0.1007-0.1499-0.0406-0.1415-0.0552-3.704215.054735.9731
63.0789-0.5310.74281.6744-0.05690.9412-0.1702-0.04920.46640.00970.0869-0.0965-0.0054-0.00910.0834-0.19150.0019-0.0457-0.22130.0374-0.1495-19.751771.643937.7915
75.25456.1256-2.64727.2757-4.10128.9929-0.48053.7467-1.14810.7954-0.72410.3945-1.00350.60531.2045-0.00060.0011-0.00020.0003-0.0034-0.001-19.465786.2054-20.4487
82.83756.2183-4.248613.6274-9.31076.36151.97663.96421.20661.2308-4.1802-0.05860.8434-0.69632.2036-0.0001-0.00160.0041-0.00090.0072-0.0014-20.147316.290331.4212
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA69 - 7311 - 15
21AA92 - 12134 - 63
31AA184 - 289126 - 231
42AA147 - 15789 - 99
52AA167 - 183109 - 125
63AA74 - 8916 - 31
73AA292 - 692234 - 634
84BB69 - 7311 - 15
94BB92 - 12134 - 63
104BB184 - 289126 - 231
115BB147 - 15789 - 99
125BB167 - 183109 - 125
136BB74 - 8916 - 31
146BB292 - 692234 - 634
157AC9011
168BD9011

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