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Yorodumi- PDB-1j2r: Crystal structure of Escherichia coli gene product Yecd at 1.3 A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j2r | ||||||
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Title | Crystal structure of Escherichia coli gene product Yecd at 1.3 A resolution | ||||||
Components | Hypothetical isochorismatase family protein yecD | ||||||
Keywords | Structural genomics / unknown function / parallel beta-sheet 3-2-1-4-5-6 / alpha-beta-alpha motif / tetramere / Bacterial targets at IGS-CNRS / France / BIGS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Suhre, K. / Claverie, J.-M. / Abergel, C. / Bacterial targets at IGS-CNRS, France (BIGS) | ||||||
Citation | Journal: To be published Title: Crystal structure of escherichia coli gene product Yecd at 1.3 A resolution Authors: Suhre, K. / Claverie, J.-M. / Abergel, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j2r.cif.gz | 172.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j2r.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j2r_validation.pdf.gz | 476.4 KB | Display | wwPDB validaton report |
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Full document | 1j2r_full_validation.pdf.gz | 482.1 KB | Display | |
Data in XML | 1j2r_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 1j2r_validation.cif.gz | 57.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/1j2r ftp://data.pdbj.org/pub/pdb/validation_reports/j2/1j2r | HTTPS FTP |
-Related structure data
Related structure data | 1im5S 1nbaS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 21794.713 Da / Num. of mol.: 4 / Mutation: A103T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yecD / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P37347, UniProt: P0ADI7*PLUS #2: Chemical | ChemComp-MPD / ( #3: Water | ChemComp-HOH / | |
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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: 2.03 Å3/Da / Density % sol: 39.06 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.5 Details: MPD, TRIS, acetate, NaCl, Lysine, pH 5.5, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50.77 Å / Num. all: 190258 / Num. obs: 163406 / % possible obs: 85.9 % / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 18.62 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.064 / Num. unique all: 13256 / % possible all: 72.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1NBA and 1IM5 Resolution: 1.3→50.77 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.686 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Hydrogens have been added in the riding positions. The structure was refined also with BUSTER, CNS and ARPWARP.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.354 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→50.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20 /
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