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Yorodumi- PDB-6hzi: Apo structure of TP domain from Burkholderia pseudomallei penicil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hzi | ||||||
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Title | Apo structure of TP domain from Burkholderia pseudomallei penicillin-binding protein 3 | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | PEPTIDE BINDING PROTEIN / penicillin-binding protein / peptidoglycan / Transpeptidase | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Apo structure of TP domain from Burkholderia pseudomallei penicillin-binding protein 3 Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hzi.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hzi.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 6hzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/6hzi ftp://data.pdbj.org/pub/pdb/validation_reports/hz/6hzi | HTTPS FTP |
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-Related structure data
Related structure data | 5uy7S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 39750.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: ftsI, CXQ84_03210, DP46_2053 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A069B4K9, UniProt: Q63QJ1*PLUS, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 25% (w/v) polyethylene glycol 3,350 and 0.3 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→53.2 Å / Num. obs: 25371 / % possible obs: 100 % / Redundancy: 25.6 % / Rrim(I) all: 0.311 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.29→2.33 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5uy7 Resolution: 2.29→53.2 Å / Cor.coef. Fo:Fc: 0.956 / SU B: 5.679 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / ESU R: 0.184 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: 45.754 Å2
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Refinement step | Cycle: 1 / Resolution: 2.29→53.2 Å
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Refine LS restraints |
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