[English] 日本語
Yorodumi- PDB-3wwn: Crystal structure of LysZ from Thermus thermophilus complex with LysW -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wwn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of LysZ from Thermus thermophilus complex with LysW | ||||||
Components |
| ||||||
Keywords | METAL BINDING PROTEIN/TRANSFERASE / Zinc finger / Amino acid kinase / METAL BINDING PROTEIN-TRANSFERASE complex | ||||||
Function / homology | Function and homology information [amino-group carrier protein]-L-2-aminoadipate 6-kinase / N2-acetyl-L-aminoadipate kinase activity / lysine biosynthetic process via aminoadipic acid / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB27 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Yoshida, A. / Tomita, T. / Kuzuyama, T. / Nishiyama, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ·LysW complex from Thermus thermophilus. Authors: Yoshida, A. / Tomita, T. / Fujimura, T. / Nishiyama, C. / Kuzuyama, T. / Nishiyama, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wwn.cif.gz | 138.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wwn.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wwn_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3wwn_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 3wwn_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 3wwn_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/3wwn ftp://data.pdbj.org/pub/pdb/validation_reports/ww/3wwn | HTTPS FTP |
-Related structure data
Related structure data | 3wwlSC 3wwmC 3u6uS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29134.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O50147 |
---|---|
#2: Protein | Mass: 5814.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9ZND7 |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.33 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% (v/w) PEG 8000, 0.1M MES pH 6.0, 0.2M Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2009 |
Radiation | Monochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 32240 / Num. obs: 32177 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Rsym value: 0.067 / Net I/σ(I): 46.9 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1582 / Rsym value: 0.72 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3WWL and 3U6U Resolution: 1.85→28.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.027 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.119 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.605 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→28.77 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.849→1.896 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|