[English] 日本語
Yorodumi- PDB-3gwm: Crystal structure of the holo-[Acyl-Carrier-Protein] Synthase (AC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gwm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the holo-[Acyl-Carrier-Protein] Synthase (ACPS) from Mycobacterium smegmatis | ||||||
Components | Holo-[acyl-carrier-protein] synthase | ||||||
Keywords | TRANSFERASE / Homo-trimer / 9-stand pseudo beta barrel protein / Cytoplasm / Fatty acid biosynthesis / Lipid synthesis / Magnesium / Metal-binding | ||||||
Function / homology | Function and homology information holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å | ||||||
Authors | Poulsen, C. / Wilmanns, M. / Song, Y.H. | ||||||
Citation | Journal: To be Published Title: Structure of the holo-[Acyl-Carrier-Protein] Synthase (ACPS) from Mycobacterium Authors: Poulsen, C. / Wilmanns, M. / Song, Y.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gwm.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gwm.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 3gwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gwm_validation.pdf.gz | 426 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3gwm_full_validation.pdf.gz | 426.1 KB | Display | |
Data in XML | 3gwm_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 3gwm_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/3gwm ftp://data.pdbj.org/pub/pdb/validation_reports/gw/3gwm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14054.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 References: UniProt: A0R1H6, holo-[acyl-carrier-protein] synthase | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.11 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM Bis-Tris pH 6.5, 16% PEG 400, 200mM (NH4)SO4, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 32734 / Rmerge(I) obs: 0.094 / D res high: 2.1 Å / Num. obs: 8718 / % possible obs: 99.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→25 Å / Num. all: 16195 / Num. obs: 15966 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 26.967 Å2 / Rmerge(I) obs: 0.047 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2 / Num. measured obs: 2864 / Num. unique all: 1207 / Num. unique obs: 1080 / % possible all: 89.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS / Resolution: 1.7→21.851 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.862 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.365 Å2 / ksol: 0.438 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.41 Å2 / Biso mean: 25.937 Å2 / Biso min: 7.07 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→21.851 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
|