[English] 日本語
Yorodumi- PDB-6lcn: Crystal structure of Serine Acetyltransferase from Planctomyces l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lcn | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Serine Acetyltransferase from Planctomyces limnophilus at 2.15A | |||||||||
Components | Serine O-acetyltransferase | |||||||||
Keywords | TRANSFERASE / PSI-Biology / IFN / Structural Genomics | |||||||||
Function / homology | Serine acetyltransferase, N-terminal domain superfamily / serine O-acetyltransferase / serine O-acetyltransferase activity / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / DI(HYDROXYETHYL)ETHER / Serine O-acetyltransferase Function and homology information | |||||||||
Biological species | Planctopirus limnophila DSM 3776 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Kumar, N. / Singh, R.P. / Singh, A.K. / Kumaran, S. | |||||||||
Funding support | India, 2items
| |||||||||
Citation | Journal: To Be Published Title: Understanding Mechanics of competitive-allostery Using Engineered Cysteine Synthase Assembly Authors: Kumar, N. / Singh, R.P. / Kumaran, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6lcn.cif.gz | 384 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6lcn.ent.gz | 300.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lcn_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6lcn_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 6lcn_validation.xml.gz | 69.7 KB | Display | |
Data in CIF | 6lcn_validation.cif.gz | 98.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/6lcn ftp://data.pdbj.org/pub/pdb/validation_reports/lc/6lcn | HTTPS FTP |
-Related structure data
Related structure data | 3f1xS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36859.645 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planctopirus limnophila DSM 3776 (bacteria) Strain: DSM 3776 / Gene: Plim_1307 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D5SUT9, serine O-acetyltransferase #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-PEG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.56 % |
---|---|
Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH=6.5, 12% w/v PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→47.596 Å / Num. obs: 120745 / % possible obs: 99.64 % / Redundancy: 4.7 % / Biso Wilson estimate: 32.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09531 / Rpim(I) all: 0.04956 / Rrim(I) all: 0.1078 / Net I/σ(I): 14.44 |
Reflection shell | Resolution: 2.15→2.227 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.742 / Num. unique obs: 11863 / CC1/2: 0.658 / Rpim(I) all: 0.3909 / Rrim(I) all: 0.8414 / % possible all: 99.23 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F1X Resolution: 2.15→47.596 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.78 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.204 / ESU R Free: 0.172 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.87 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→47.596 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|