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Yorodumi- PDB-5gkv: Crystal Structure of a Novel Penicillin-Binding Protein (PBP) Hom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gkv | ||||||
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Title | Crystal Structure of a Novel Penicillin-Binding Protein (PBP) Homolog from Caulobacter crescentus | ||||||
Components | Esterase A | ||||||
Keywords | HYDROLASE / Penicillin-binding protein / biochemical assay | ||||||
Function / homology | Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / peptidase activity / Esterase A Function and homology information | ||||||
Biological species | Caulobacter crescentus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.901 Å | ||||||
Authors | Ngo, T.D. / Ryu, B.H. / Kim, B.Y. / Yoo, W.K. / Lee, E.J. / Lee, S.J. / Kim, T.D. / Kim, K.K. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Biochemical and Structural Analysis of a Novel Penicillin-Binding Protein (PBP) Homolog from Caulobacter crescentus Authors: Ryu, B.H. / Ngo, T.D. / Kim, B.Y. / Yoo, W.K. / Lee, E.J. / Lee, S.J. / Kim, K.K. / Kim, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gkv.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gkv.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/5gkv ftp://data.pdbj.org/pub/pdb/validation_reports/gk/5gkv | HTTPS FTP |
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-Related structure data
Related structure data | 3zytS 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
#1: Protein | Mass: 41345.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter crescentus (strain ATCC 19089 / CB15) (bacteria) Strain: ATCC 19089 / CB15 / Gene: CC_0255 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ABH2 |
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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: 2.18 Å3/Da / Density % sol: 43.69 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 50mM potassium phosphate monobasic, 20%(w/v) polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.919805 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919805 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 29140 / % possible obs: 99.99 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 34.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZYT Resolution: 1.901→29.144 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.48 Å2 / Biso mean: 24.572 Å2 / Biso min: 10.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.901→29.144 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: 14
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