+Open data
-Basic information
Entry | Database: PDB / ID: 3wwm | ||||||
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Title | Crystal structure of LysZ from Thermus thermophilus with ADP | ||||||
Components | Putative acetylglutamate kinase-like protein | ||||||
Keywords | TRANSFERASE / Amino acid kinase | ||||||
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 / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB27 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wwm.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wwm.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 3wwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/3wwm ftp://data.pdbj.org/pub/pdb/validation_reports/ww/3wwm | HTTPS FTP |
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-Related structure data
Related structure data | 3wwlC 3wwnC 3u6uS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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) / Gene: TT_C1541 / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O50147 |
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#2: Chemical | ChemComp-ADP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.1M tri-sodium citrate, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2010 |
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: 2.8→50 Å / Num. all: 13007 / Num. obs: 13002 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Rsym value: 0.049 / Net I/σ(I): 59.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 8.7 / Num. unique all: 2355 / Rsym value: 0.394 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U6U Resolution: 2.8→42.94 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.212 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.494 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→42.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.799→2.872 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 15.4882 Å / Origin y: -1.4117 Å / Origin z: 24.546 Å
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