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Yorodumi- PDB-2g2p: Crystal Structure of E.coli transthyretin-related protein with bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g2p | ||||||
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Title | Crystal Structure of E.coli transthyretin-related protein with bound Zn and Br | ||||||
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: 2.1 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 | 2g2p.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g2p.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 2g2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g2p_validation.pdf.gz | 462.5 KB | Display | wwPDB validaton report |
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Full document | 2g2p_full_validation.pdf.gz | 464 KB | Display | |
Data in XML | 2g2p_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 2g2p_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/2g2p ftp://data.pdbj.org/pub/pdb/validation_reports/g2/2g2p | HTTPS FTP |
-Related structure data
Related structure data | 2g2nC 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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1 |
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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 | ChemComp-BR / #4: Chemical | ChemComp-SO4 / #5: 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: 2.21 Å3/Da / Density % sol: 44.25 % |
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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 (Crystal soaked in crystallization buffer enriched with 100mM NaBr for 12h prior to data collection), 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: 2.1→20 Å / Num. all: 25512 / Num. obs: 25512 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.1→2.3 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 10 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F41 Resolution: 2.1→17.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.024 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.197 / 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: 19.438 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→17.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.104→2.158 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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