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- PDB-7bn9: Crystal Structure of Bacillus subtilis Penicillin Binding Protein 3 -

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Basic information

Entry
Database: PDB / ID: 7bn9
TitleCrystal Structure of Bacillus subtilis Penicillin Binding Protein 3
ComponentsPenicillin-binding protein 3
KeywordsHYDROLASE / Transpeptidase / penicillin-binding protein / low-affinity / peptidoglycan
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic
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
Penicillin-binding protein 3
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsRao, V.A. / Lewis, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N002679/1 United Kingdom
CitationJournal: To Be Published
Title: Cooperation between peptidoglycan transpeptidases and SEDS proteins in Bacillus subtilis cell division
Authors: Sassine, J. / Rao, V.A. / Goldsmith, G. / Breukink, E. / Lewis, R.J. / Daniel, R.A. / Vollmer, W.
History
DepositionJan 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein 3
B: Penicillin-binding protein 3


Theoretical massNumber of molelcules
Total (without water)148,0412
Polymers148,0412
Non-polymers00
Water1,76598
1
A: Penicillin-binding protein 3


Theoretical massNumber of molelcules
Total (without water)74,0201
Polymers74,0201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 3


Theoretical massNumber of molelcules
Total (without water)74,0201
Polymers74,0201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.624, 108.684, 238.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Penicillin-binding protein 3 / PBP 3 / PSPB20 / Penicillin-binding protein C


Mass: 74020.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: pbpC, ycsM, yzsA, BSU04140
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P42971, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 20 % (w/v) PEG 6000, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→49.46 Å / Num. obs: 42319 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 59.24 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.7
Reflection shellResolution: 2.65→9.92 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4375 / CC1/2: 0.639 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VQQ, 3EQU

1vqq

3equ


Resolution: 2.65→49.46 Å / SU ML: 0.3984 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.269 2165 5.12 %
Rwork0.213 40154 -
obs0.2159 42319 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.61 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9181 0 0 98 9279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039353
X-RAY DIFFRACTIONf_angle_d0.696412670
X-RAY DIFFRACTIONf_chiral_restr0.04791414
X-RAY DIFFRACTIONf_plane_restr0.00451640
X-RAY DIFFRACTIONf_dihedral_angle_d5.8781270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.710.37731230.30682651X-RAY DIFFRACTION99.96
2.71-2.780.35951330.27872619X-RAY DIFFRACTION99.96
2.78-2.850.3261430.2772650X-RAY DIFFRACTION100
2.85-2.940.37681320.27452612X-RAY DIFFRACTION100
2.94-3.030.36251310.26692692X-RAY DIFFRACTION100
3.03-3.140.36551470.26562598X-RAY DIFFRACTION99.96
3.14-3.270.3171460.26762666X-RAY DIFFRACTION100
3.27-3.420.30441470.23832672X-RAY DIFFRACTION100
3.42-3.60.31171520.23012639X-RAY DIFFRACTION100
3.6-3.820.26111420.21062651X-RAY DIFFRACTION100
3.82-4.120.25331420.1872674X-RAY DIFFRACTION100
4.12-4.530.21641580.16772714X-RAY DIFFRACTION100
4.53-5.190.21791530.17462682X-RAY DIFFRACTION100
5.19-6.530.2481610.21182730X-RAY DIFFRACTION100
6.53-49.460.23431550.19052904X-RAY DIFFRACTION99.97

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