+Open data
-Basic information
Entry | Database: PDB / ID: 6syn | ||||||
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Title | Crystal structure of Y. pestis penicillin-binding protein 3 | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | CYTOSOLIC PROTEIN / Class B PBP / Yersinia pestis / HMM transpeptidase / periplasmic protein | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape ...peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / membrane => GO:0016020 / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.63 Å | ||||||
Authors | Pankov, G. / Hunter, W.N. / Dawson, A. | ||||||
Citation | Journal: To Be Published Title: The structure of penicillin-binding protein 3 from Yersinia pestis Authors: Pankov, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6syn.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6syn.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 6syn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6syn_validation.pdf.gz | 838.7 KB | Display | wwPDB validaton report |
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Full document | 6syn_full_validation.pdf.gz | 842.1 KB | Display | |
Data in XML | 6syn_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 6syn_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/6syn ftp://data.pdbj.org/pub/pdb/validation_reports/sy/6syn | HTTPS FTP |
-Related structure data
Related structure data | 6tudC 4bjpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57646.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ftsI, YPO0549 / Production host: Escherichia coli (E. coli) References: UniProt: Q0WJB8, UniProt: A0A3N4B5A3*PLUS, serine-type D-Ala-D-Ala carboxypeptidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CB9 / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 40 % / Description: rectangular prisms |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.2 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 6.7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5 and 20% PEG 8000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→36 Å / Num. obs: 14613 / % possible obs: 98.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 8.1 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.097 / Rrim(I) all: 0.153 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.63→2.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1663 / CC1/2: 0.652 / Rpim(I) all: 0.203 / Rrim(I) all: 0.312 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BJP Resolution: 2.63→36 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.819 / SU B: 13.841 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.382 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62 Å2 / Biso mean: 15.899 Å2 / Biso min: 5 Å2
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Refinement step | Cycle: final / Resolution: 2.63→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.63→2.696 Å / Rfactor Rfree error: 0
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