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- PDB-8e2c: N-terminal domain of S. aureus GpsB in complex with PBP4 fragment -
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Open data
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Basic information
Entry | Database: PDB / ID: 8e2c | ||||||
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Title | N-terminal domain of S. aureus GpsB in complex with PBP4 fragment | ||||||
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![]() | PEPTIDE BINDING PROTEIN / Peptidoglycan / PBP / PBP4 / MRSA / GpsB / PBP2a cell wall / transpeptidase / b-lactam / gram-positive / sporulation / cell division / bacterial cell division / diviva / divisome | ||||||
Function / homology | Cell cycle protein GpsB / DivIVA family / DivIVA domain / DivIVA protein / regulation of cell shape / cell cycle / cell division / cytoplasm / Cell cycle protein GpsB![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sacco, M. / Chen, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Staphylococcus aureus FtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB. Authors: Sacco, M.D. / Hammond, L.R. / Noor, R.E. / Bhattacharya, D. / McKnight, L.J. / Madsen, J.J. / Zhang, X. / Butler, S.G. / Kemp, M.T. / Jaskolka-Brown, A.C. / Khan, S.J. / Gelis, I. / Eswara, P. / Chen, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.6 KB | Display | ![]() |
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PDB format | ![]() | 28.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.8 KB | Display | ![]() |
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Full document | ![]() | 426.9 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8e2bC ![]() 4ug3S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8328.440 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: COL / Gene: gpsB, SACOL1484 Production host: ![]() ![]() References: UniProt: Q5HFX8 #2: Protein/peptide | | Mass: 993.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pbp4 Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.31 % / Description: Plate-like |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25 % PEG 4000, 0.1 M Tris pH 8.0, and 0.2 M Na Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→41.19 Å / Num. obs: 6596 / % possible obs: 95.7 % / Redundancy: 5.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.048 / Rrim(I) all: 0.113 / Net I/σ(I): 10.8 / Num. measured all: 34441 / Scaling rejects: 198 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4UG3 Resolution: 2.4→36.91 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.727 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.523 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.33 Å2 / Biso mean: 38.619 Å2 / Biso min: 19.71 Å2
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Refinement step | Cycle: final / Resolution: 2.4→36.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.463 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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