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Yorodumi- PDB-3vwo: Crystal structure of peptidoglycan hydrolase mutant from Sphingom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vwo | ||||||
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Title | Crystal structure of peptidoglycan hydrolase mutant from Sphingomonas sp. A1 | ||||||
Components | Peptidoglycan hydrolase FlgJ | ||||||
Keywords | HYDROLASE / peptidoglycan hydrolase | ||||||
Function / homology | Function and homology information amidase activity / hydrolase activity, acting on glycosyl bonds / bacterial-type flagellum assembly / metabolic process / periplasmic space Similarity search - Function | ||||||
Biological species | Sphingomonas sp. A1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å | ||||||
Authors | Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
Citation | Journal: To be Published Title: Crystal structure of peptidoglycan hydrolase mutant from Sphingomonas sp. A1 Authors: Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vwo.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vwo.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/3vwo ftp://data.pdbj.org/pub/pdb/validation_reports/vw/3vwo | HTTPS FTP |
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-Related structure data
Related structure data | 2zycS 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: 17957.908 Da / Num. of mol.: 1 / Fragment: UNP residues 154-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Gene: flgJ / Production host: Escherichia coli (E. coli) / References: UniProt: B7XH69 |
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#2: Chemical | ChemComp-EPE / |
#3: 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: 2.03 Å3/Da / Density % sol: 39.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 1.0M NaCitrate, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 14387 / Num. obs: 14387 / % possible obs: 99.6 % / Redundancy: 9.6 % / Rsym value: 0.051 / Net I/σ(I): 55.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 679 / Rsym value: 0.312 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2zyc Resolution: 1.802→26.4 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 23.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.772 Å2 / ksol: 0.421 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.802→26.4 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: 5
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