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Yorodumi- PDB-6tii: Crystal structure of penicillin-binding protein 2 from Yersinia pestis -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tii | ||||||
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Title | Crystal structure of penicillin-binding protein 2 from Yersinia pestis | ||||||
Components | Peptidoglycan D,D-transpeptidase MrdA | ||||||
Keywords | MEMBRANE PROTEIN / Class B PBP / Yersinia pestis / HMM transpeptidase / periplasmic protein / peptidoglycan crosslinking | ||||||
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 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Pankov, G. / Hunter, W.N. / Dawson, A. | ||||||
Citation | Journal: To Be Published Title: The structure of penicillin-binding protein 2 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 | 6tii.cif.gz | 235.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tii.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tii_validation.pdf.gz | 442 KB | Display | wwPDB validaton report |
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Full document | 6tii_full_validation.pdf.gz | 453.2 KB | Display | |
Data in XML | 6tii_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 6tii_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/6tii ftp://data.pdbj.org/pub/pdb/validation_reports/ti/6tii | HTTPS FTP |
-Related structure data
Related structure data | 6xv5C 5lp4S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains A B) |
-Components
#1: Protein | Mass: 65552.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: mrdA, YPO2604 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A384KFW3, UniProt: A0A5P8YJF3*PLUS, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.4 % / Description: Branched rectangular prisms |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 1 uL of 1 mg/ml YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 2 uL reservoir solution (containing 0.1 M HEPES-NaOH pH 7.5, 0.5 M K+/Na+ tartrate and 10 mM NaBr) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→79.36 Å / Num. obs: 56420 / % possible obs: 90.2 % / Redundancy: 5.5 % / CC1/2: 0.781 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.095 / Rrim(I) all: 0.163 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.2→2.26 Å / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4462 / CC1/2: 0.703 / Rpim(I) all: 0.632 / Rrim(I) all: 0.756 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LP4 Resolution: 2.26→50.005 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.2 / SU ML: 0.255 / Cross valid method: FREE R-VALUE / ESU R: 0.353 / ESU R Free: 0.252 Details: Hydrogens have been added in their riding positions
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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 mean: 50.592 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→50.005 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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