+Open data
-Basic information
Entry | Database: PDB / ID: 4lzh | ||||||
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Title | L,D-transpeptidase from Klebsiella pneumoniae | ||||||
Components | L,D-transpeptidase | ||||||
Keywords | TRANSFERASE / structural genomics / APC110661 / L / D-transpeptidase / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | L,D-transpeptidase C-terminal domain / L,D-transpeptidase C-terminal domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / peptidoglycan biosynthetic process / transferase activity / periplasmic space / Uncharacterized protein Function and homology information | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Osipiuk, J. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: L,D-transpeptidase from Klebsiella pneumoniae. Authors: Osipiuk, J. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lzh.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lzh.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 4lzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/4lzh ftp://data.pdbj.org/pub/pdb/validation_reports/lz/4lzh | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31325.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: MGH 78578 / Gene: KPN78578_08240, KPN_00849, ybiS / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6T6R4 |
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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: 3.01 Å3/Da / Density % sol: 59.08 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1 M k/Na tartrate, 0.1 M Tris buffer, 0.2 M lithium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→37.7 Å / Num. all: 28687 / Num. obs: 28687 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.143 / Χ2: 1.599 / Net I/σ(I): 8.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→37.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.26 / SU B: 4.709 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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: 86.34 Å2 / Biso mean: 26.383 Å2 / Biso min: 9.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→37.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 35.2636 Å / Origin y: 20.2237 Å / Origin z: 10.741 Å
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