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- PDB-6g88: Crystal structure of Enterococcus Faecium D63r Penicillin-Binding... -

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Basic information

Entry
Database: PDB / ID: 6g88
TitleCrystal structure of Enterococcus Faecium D63r Penicillin-Binding protein 5 (PBP5fm)
ComponentsLow affinity penicillin-binding protein 5 (PBP5)
KeywordsANTIBIOTIC / penicillin-binding / ceftobiprole / Enterococcus faecium / Antibiotic resistance
Function / homology
Function and homology information


penicillin binding / response to antibiotic / plasma membrane
Similarity search - Function
NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / NTF2-like domain superfamily / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-RB6 / Low affinity penicillin-binding protein 5 (PBP5)
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsSauvage, E. / El Gachi, M. / Herman, R. / Kerff, F. / Charlier, P.
CitationJournal: To Be Published
Title: Structural basis of inactivation of Enterococcus faecium penicillin binding protein 5 by ceftobiprole.
Authors: Sauvage, E. / El Gachi, M. / Kerff, F. / Herman, R. / Verlaine, O. / Amoroso, A. / Page, M.G.P. / Joris, B. / Charlier, P.
History
DepositionApr 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low affinity penicillin-binding protein 5 (PBP5)
B: Low affinity penicillin-binding protein 5 (PBP5)
C: Low affinity penicillin-binding protein 5 (PBP5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,1299
Polymers212,2313
Non-polymers1,8986
Water0
1
A: Low affinity penicillin-binding protein 5 (PBP5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3763
Polymers70,7441
Non-polymers6332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Low affinity penicillin-binding protein 5 (PBP5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3763
Polymers70,7441
Non-polymers6332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Low affinity penicillin-binding protein 5 (PBP5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3763
Polymers70,7441
Non-polymers6332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.194, 128.736, 238.479
Angle α, β, γ (deg.)90.00, 94.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Low affinity penicillin-binding protein 5 (PBP5)


Mass: 70743.773 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: pbp5 / Production host: Enterococcus faecium (bacteria) / References: UniProt: Q47759
#2: Chemical ChemComp-RB6 / (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyrrolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / BAL 9141, bound form / ceftobiprole, bound form


Mass: 536.585 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H24N8O6S2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 293 K / Method: evaporation
Details: Crystals were grown by the sitting-drop vapor diffusion method. Crystals were grown at 20C by mixing 1microL of PBP5fm (48 mg/ml), 2microL of reservoir (20% PEG8000 (w/v), 0.4 M Li2SO4 and ...Details: Crystals were grown by the sitting-drop vapor diffusion method. Crystals were grown at 20C by mixing 1microL of PBP5fm (48 mg/ml), 2microL of reservoir (20% PEG8000 (w/v), 0.4 M Li2SO4 and 100 mM Na acetate at pH 4.5) and 0.5 microL of 0.1M ceftobiprole (kind gift of Basilea Pharmaceutica. The crystal was cryoprotected in the same buffer containing 20 % (v/v) glycerol. Crystals were soaked for 5 min in 1 microl of 0.1 M ceftobiprole before cryoprotection.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.3→47.58 Å / Num. obs: 35868 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.14 / Rrim(I) all: 0.277 / Net I/σ(I): 5.4
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.767 / Num. unique obs: 5148 / Rpim(I) all: 0.449 / Rrim(I) all: 0.891 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementResolution: 3.3→47.577 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 1802 5.02 %
Rwork0.2003 --
obs0.2029 35861 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→47.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13793 0 123 0 13916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414129
X-RAY DIFFRACTIONf_angle_d0.91319107
X-RAY DIFFRACTIONf_dihedral_angle_d12.9118630
X-RAY DIFFRACTIONf_chiral_restr0.052149
X-RAY DIFFRACTIONf_plane_restr0.0052510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.38930.34251220.27192568X-RAY DIFFRACTION99
3.3893-3.4890.30691470.26192561X-RAY DIFFRACTION100
3.489-3.60160.33431470.23412689X-RAY DIFFRACTION100
3.6016-3.73030.26611080.23082569X-RAY DIFFRACTION100
3.7303-3.87960.25221420.21472597X-RAY DIFFRACTION100
3.8796-4.0560.28851210.20862617X-RAY DIFFRACTION100
4.056-4.26980.21731330.18482650X-RAY DIFFRACTION100
4.2698-4.53710.21651360.17142617X-RAY DIFFRACTION100
4.5371-4.88710.21781470.16592597X-RAY DIFFRACTION100
4.8871-5.37830.22411600.17532656X-RAY DIFFRACTION100
5.3783-6.15510.26921380.20162628X-RAY DIFFRACTION100
6.1551-7.74930.27791430.20412630X-RAY DIFFRACTION100
7.7493-47.5820.20941580.18172680X-RAY DIFFRACTION100
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)
12.1144-0.893-0.37723.0575-0.75251.988-0.02410.2406-0.00050.29460.01480.1601-0.0126-0.17510.00290.40830.15610.01160.4466-0.07020.3811-44.220711.446426.9064
20.6891-0.25330.15960.1833-0.1360.5380.0990.0682-0.5107-0.04610.01120.31770.22710.0759-0.22410.60320.1427-0.06880.4233-0.07090.6779-31.8089-24.828144.8287
30.6693-0.55060.72050.5664-0.24242.4342-0.04160.0235-0.19780.0570.08560.0280.0027-0.1644-0.06670.27850.0643-0.0050.2775-0.02620.3433-25.7367-15.440864.2588
41.2422-0.5613-0.95480.8502-0.09663.2474-0.2019-0.19940.09110.31870.29870.0301-0.6092-0.2149-0.09370.61290.2264-0.04720.3934-0.0140.4132-17.8654-12.387393.8317
51.7891-1.70710.68764.2534-0.47872.53180.28330.17250.0772-0.237-0.2762-0.11140.34770.0950.04350.38710.08480.01250.2894-0.00170.3746-30.9111-20.9032132.8186
6-0.1151-0.33580.08321.041-1.06621.09270.1159-0.0156-0.1446-0.07480.09160.35180.0634-0.0673-0.25510.467-0.01970.01030.3715-0.01550.4669-45.3224.4142118.2884
70.3541-0.2356-0.01660.8857-0.75962.99620.10190.0153-0.0942-0.1066-0.00280.12480.3555-0.0319-0.05210.28910.0164-0.00060.2323-0.00530.3661-43.25689.717495.4437
80.7833-0.3195-0.04331.07940.88913.17250.1630.1516-0.0151-0.2603-0.08490.02710.26230.1698-0.07280.38550.09260.02610.31620.040.3685-33.808417.354167.1943
93.37080.16720.30982.04750.27652.2352-0.1402-0.09050.07320.08820.18980.4568-0.1202-0.13160.030.512-0.0281-0.00640.60690.07880.5868-61.9059-18.529951.8803
101.4938-1.0709-0.21340.781-0.09831.33360.2149-0.17220.4627-0.0489-0.0834-0.2386-0.19960.3713-0.14240.3034-0.0893-0.0210.4226-0.10870.4772-28.5075-13.601337.7821
110.6785-0.2061-1.2931-0.13020.95252.70830.06610.06340.0735-0.00150.00030.0689-0.02770.0365-0.09190.32390.07230.01280.46250.00110.4188-26.1184-21.216516.8579
121.247-0.68140.10390.87180.37954.06040.00120.3725-0.0119-0.1276-0.0646-0.01120.15530.00690.08730.26020.04090.02080.5774-0.03420.3406-21.3318-31.5532-11.7101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 141 )
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 264 )
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 435 )
4X-RAY DIFFRACTION4chain 'A' and (resid 436 through 679 )
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 141 )
6X-RAY DIFFRACTION6chain 'B' and (resid 142 through 264 )
7X-RAY DIFFRACTION7chain 'B' and (resid 265 through 435 )
8X-RAY DIFFRACTION8chain 'B' and (resid 436 through 679 )
9X-RAY DIFFRACTION9chain 'C' and (resid 39 through 141 )
10X-RAY DIFFRACTION10chain 'C' and (resid 142 through 264 )
11X-RAY DIFFRACTION11chain 'C' and (resid 265 through 435 )
12X-RAY DIFFRACTION12chain 'C' and (resid 436 through 679 )

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