[English] 日本語
Yorodumi- PDB-4p7l: Structure of Escherichia coli PgaB C-terminal domain, P212121 cry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p7l | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Escherichia coli PgaB C-terminal domain, P212121 crystal form | ||||||
Components | Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase | ||||||
Keywords | HYDROLASE / beta alpha barrel / carbohydrate binding / glycosyl hydrolase fold | ||||||
Function / homology | Function and homology information macromolecule deacylation / cell adhesion involved in biofilm formation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / single-species biofilm formation / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / hydrolase activity, hydrolyzing O-glycosyl compounds / cell outer membrane / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.802 Å | ||||||
Authors | Little, D.J. / Li, G. / Ing, C. / DiFrancesco, B. / Bamford, N.C. / Robinson, H. / Nitz, M. / Pomes, R. / Howell, P.L. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Modification and periplasmic translocation of the biofilm exopolysaccharide poly-beta-1,6-N-acetyl-D-glucosamine. Authors: Little, D.J. / Li, G. / Ing, C. / DiFrancesco, B.R. / Bamford, N.C. / Robinson, H. / Nitz, M. / Pomes, R. / Howell, P.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4p7l.cif.gz | 164.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4p7l.ent.gz | 126.2 KB | Display | PDB format |
PDBx/mmJSON format | 4p7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/4p7l ftp://data.pdbj.org/pub/pdb/validation_reports/p7/4p7l | HTTPS FTP |
---|
-Related structure data
Related structure data | 4p7nC 4p7oC 4p7qC 4p7rC 4f9dS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42441.867 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 310-672) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: pgaB, ycdR, b1023, JW5142 / Plasmid: pET28A / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P75906, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
---|---|
#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.72 % / Description: Long rods |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18% PEG3350, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2012 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 30391 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 17.73 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 5.1 / % possible all: 96.4 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4F9D Resolution: 1.802→48.962 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.76 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.19 Å2 / Biso mean: 21.5705 Å2 / Biso min: 6.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.802→48.962 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|