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Yorodumi- PDB-7tbr: Crystal structure of the TPM domain from the Rhodothermus marinus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tbr | |||||||||
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Title | Crystal structure of the TPM domain from the Rhodothermus marinus protein Rhom172_1776 | |||||||||
Components | TPM_phosphatase domain-containing protein | |||||||||
Keywords | UNKNOWN FUNCTION / TPM domain | |||||||||
Function / homology | TPM domain / TPM domain / membrane / TPM_phosphatase domain-containing protein Function and homology information | |||||||||
Biological species | Rhodothermus marinus SG0.5JP17-172 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | |||||||||
Authors | Pellizza, L. / Klinke, S. / Aran, M. | |||||||||
Funding support | Argentina, 2items
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Citation | Journal: To be published Title: Crystal structure of the TPM domain from the Rhodothermus marinus protein Rhom172_1776 Authors: Pellizza, L. / Klinke, S. / Aran, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tbr.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tbr.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 7tbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tbr_validation.pdf.gz | 972.5 KB | Display | wwPDB validaton report |
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Full document | 7tbr_full_validation.pdf.gz | 974.4 KB | Display | |
Data in XML | 7tbr_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 7tbr_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/7tbr ftp://data.pdbj.org/pub/pdb/validation_reports/tb/7tbr | HTTPS FTP |
-Related structure data
Related structure data | 5anpS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15642.761 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodothermus marinus SG0.5JP17-172 (bacteria) Strain: SG0.5JP17-172 / Gene: Rhom172_1776 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G2SGJ4 |
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#2: Chemical | ChemComp-B3P / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.8 % / Description: long bars |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 12% PEG 6000, 5% isopropanol, 0.1 M Bis-tris-propane pH 8.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.885601 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2021 Details: convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors |
Radiation | Monochromator: Cryogenically cooled channel cut crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.885601 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→42.79 Å / Num. obs: 54711 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.039 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8430 / CC1/2: 0.679 / Rrim(I) all: 1.021 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ANP Resolution: 1.1→42.79 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.654 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.038 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.477 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→42.79 Å
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Refine LS restraints |
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