[English] 日本語
Yorodumi- PDB-3gek: Crystal structure of putative thioesterase yhdA from Lactococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gek | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of putative thioesterase yhdA from Lactococcus lactis. Northeast Structural Genomics Consortium Target KR113 | ||||||
Components | Putative thioesterase yhdA | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structure Genomics / NESG / KR113 / Q9CHK5_LACLA / Lactococcus lactis / yhdA / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / 4HBT domain-containing protein Function and homology information | ||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Kuzin, A.P. / Su, M. / Seetharaman, R. / Lee, D. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Nair, R. / Rost, B. ...Kuzin, A.P. / Su, M. / Seetharaman, R. / Lee, D. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Nair, R. / Rost, B. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be published Title: X-Ray structure of putative thioesterase yhdA from Lactococcus lactis. Northeast Structural Genomics Consortium Target KR113 Authors: Kuzin, A.P. / Su, M. / Seetharaman, R. / Lee, D. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Nair, R. / Rost, B. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gek.cif.gz | 109.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gek.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gek_validation.pdf.gz | 429.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3gek_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 3gek_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 3gek_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/3gek ftp://data.pdbj.org/pub/pdb/validation_reports/ge/3gek | HTTPS FTP |
-Related structure data
Related structure data | 1vh5S S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16485.957 Da / Num. of mol.: 4 / Mutation: S23F, H44Q, S70G, L75F, S80N, S86P, C96R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Strain: Il1403 / Gene: L131, L131392, LL0726, yhdA / Plasmid: pET21-23c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9CHK5 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.59 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 14% PEG 3350, 20% Ethylene glycol, 0.2M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 2009 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. obs: 51899 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2.24→2.32 Å / Redundancy: 7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 6.3 / % possible all: 87.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VH5 Resolution: 2.24→46.18 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 15.535 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.656 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→46.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.24→2.3 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 21.6703 Å / Origin y: 1.2202 Å / Origin z: -17.9207 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|