[English] 日本語
Yorodumi- PDB-3kg4: Crystal structure of an uncharacterized protein from Mannheimia s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kg4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of an uncharacterized protein from Mannheimia succiniciproducens | ||||||
Components | Uncharacterized protein | ||||||
Keywords | Structural Genomics / Unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding Similarity search - Function | ||||||
Biological species | Mannheimia succiniciproducens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Bonanno, J.B. / Dickey, M. / Bain, K.T. / Lau, C. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of an uncharacterized protein from Mannheimia succiniciproducens Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Lau, C. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kg4.cif.gz | 51 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kg4.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 3kg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/3kg4 ftp://data.pdbj.org/pub/pdb/validation_reports/kg/3kg4 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27086.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mannheimia succiniciproducens (bacteria) Strain: MBEL55E / Gene: MS0988 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q65TW5 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.34 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 5.5 Details: 100mM Bis-Tris pH 5.5, 22% PEG 3350, 200mM ammonium sulfate, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 18, 2009 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→70.864 Å / Num. all: 17315 / Num. obs: 17142 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.1 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 23.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 10.2 / Num. unique all: 2470 / Rsym value: 0.33 / % possible all: 98.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.222 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.836 / SU B: 3.399 / SU ML: 0.1 / SU R Cruickshank DPI: 0.16 / SU Rfree: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.16 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.62 Å2 / Biso mean: 36.145 Å2 / Biso min: 12.59 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
|