[English] 日本語
Yorodumi- PDB-5cj5: Structure of Mycobacterium thermoresistibile GlgE APO form at 3.1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cj5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Mycobacterium thermoresistibile GlgE APO form at 3.13A resolution | ||||||
Components | Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | ||||||
Keywords | TRANSFERASE / GlgE / Maltose / GH13 / maltosyltransferase | ||||||
Function / homology | Function and homology information starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / hexosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | ||||||
Biological species | Mycobacterium thermoresistibile ATCC 19527 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.13 Å | ||||||
Authors | Mendes, V. / Blaszczyk, M. / Maranha, A. / Empadinhas, N. / Blundell, T.L. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Structure of Mycobacterium thermoresistibile GlgE defines novel conformational states that contribute to the catalytic mechanism. Authors: Mendes, V. / Blaszczyk, M. / Maranha, A. / Empadinhas, N. / Blundell, T.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5cj5.cif.gz | 267.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5cj5.ent.gz | 216.6 KB | Display | PDB format |
PDBx/mmJSON format | 5cj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cj5_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5cj5_full_validation.pdf.gz | 539.7 KB | Display | |
Data in XML | 5cj5_validation.xml.gz | 57.1 KB | Display | |
Data in CIF | 5cj5_validation.cif.gz | 77.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/5cj5 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/5cj5 | HTTPS FTP |
-Related structure data
Related structure data | 5cgmSC 5cimC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 0 - 696 / Label seq-ID: 2 - 698
|
-Components
#1: Protein | Mass: 77618.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium thermoresistibile ATCC 19527 (bacteria) Gene: glgE, KEK_12948 / Production host: Escherichia coli (E. coli) References: UniProt: G7CL00, starch synthase (maltosyl-transferring) |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.94 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Bicine pH9.5, Sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.978 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.13→171.16 Å / Num. all: 41628 / Num. obs: 41628 / % possible obs: 100 % / Redundancy: 13.5 % / Rpim(I) all: 0.063 / Rrim(I) all: 0.234 / Rsym value: 0.218 / Net I/av σ(I): 3.268 / Net I/σ(I): 13 / Num. measured all: 563635 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _ / % possible all: 100
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CGM Resolution: 3.13→171.16 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.63 / Stereochemistry target values: TWIN_LSQ_F
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 211.41 Å2 / Biso mean: 73.8803 Å2 / Biso min: 22.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.13→171.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
|