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Yorodumi- PDB-1okj: crystal structure of the essential E. coli YeaZ protein by MAD me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1okj | ||||||
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Title | crystal structure of the essential E. coli YeaZ protein by MAD method using the gadolinium complex "DOTMA" | ||||||
Components | TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB | ||||||
Keywords | HYDROLASE / POTENTIAL ZINC PROTEASE / HYPOTHETICAL PROTEASE YEAZ / METALLOPROTEASE / BACTERIAL TARGETS AT IGS-CNRS / FRANCE / BIGS / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / maintenance of translational fidelity / metallopeptidase activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.28 Å | ||||||
Authors | Abergel, C. / Jeudy, S. / Claverie, J.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: A Complement to the Modern Crystallographer'S Toolbox: Caged Gadolinium Complexes with Versatile Binding Modes. Authors: Stelter, M. / Molina, R. / Jeudy, S. / Kahn, R. / Abergel, C. / Hermoso, J.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Preliminary Crystallographic Analysis of the Escherichia Coli Yeaz Protein Using the Anomalous Signal of a Gadolinium Derivative. Authors: Jeudy, S. / Stelter, M. / Coutard, B. / Kahn, R. / Abergel, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1okj.cif.gz | 177.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1okj.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 1okj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/1okj ftp://data.pdbj.org/pub/pdb/validation_reports/ok/1okj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27609.381 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: GATEWAY PEPTIDE INSERTED ON THE PROTEIN SEQUENCE FOR PROTEIN EXPRESSION AND PURIFICATION Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P76256, Hydrolases; Acting on peptide bonds (peptidases) #2: Chemical | ChemComp-GD3 / #3: Water | ChemComp-HOH / | Sequence details | N-TERMINAL INSERTION OF THE GATEWAY PEPTIDE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | pH: 4.7 Details: PEG 8000, NA ACETATE 0.1M PH 4.7, NACL 0.2M, GLYCEROL 10% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.71058 |
Detector | Date: Jun 15, 2003 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.71058 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→19.85 Å / Num. obs: 48235 / % possible obs: 98.3 % / Redundancy: 5 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.28→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: 14 C-TERMINUS RESIDUES AND 20 GATEWAY N-TERMINUS RESIDUES DISORDERED IN THE 4 MOLECULES OF THE AU
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.5533 Å2 / ksol: 0.359104 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.28→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.42 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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