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Yorodumi- PDB-2g2n: Crystal Structure of E.coli transthyretin-related protein with bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g2n | ||||||
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Title | Crystal Structure of E.coli transthyretin-related protein with bound Zn | ||||||
Components | Transthyretin-like protein | ||||||
Keywords | UNKNOWN FUNCTION / Transthyretin / Transthyretin-related protein | ||||||
Function / homology | Function and homology information hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / purine nucleobase metabolic process / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Lundberg, E. / Backstrom, S. / Sauer, U.H. / Sauer-Eriksson, A.E. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2006 Title: The transthyretin-related protein: structural investigation of a novel protein family Authors: Lundberg, E. / Backstrom, S. / Sauer, U.H. / Sauer-Eriksson, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g2n.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g2n.ent.gz | 84.6 KB | Display | PDB format |
PDBx/mmJSON format | 2g2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g2n_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 2g2n_full_validation.pdf.gz | 454.9 KB | Display | |
Data in XML | 2g2n_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 2g2n_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/2g2n ftp://data.pdbj.org/pub/pdb/validation_reports/g2/2g2n | HTTPS FTP |
-Related structure data
Related structure data | 2g2pC 1f41S 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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2 |
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Unit cell |
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Details | The asymmetric unit contains one biological tetramer |
-Components
#1: Protein | Mass: 13029.600 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / References: UniProt: P76341 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.25 Å3/Da / Density % sol: 45.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 550 MME, 100mM MES, 10mM ZnSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8033 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 6, 2001 |
Radiation | Monochromator: Triangular Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8033 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→17.05 Å / Num. all: 44377 / Num. obs: 44377 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.65→1.69 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.4 / % possible all: 90.3 |
-Processing
Software | Name: REFMAC / Version: 5.1.27 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F41 Resolution: 1.65→17.05 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.902 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 15.515 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→17.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.692 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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