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Yorodumi- PDB-5ere: Extracellular ligand binding receptor from Desulfohalobium retbae... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ere | ||||||
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Title | Extracellular ligand binding receptor from Desulfohalobium retbaense DSM5692 | ||||||
Components | Extracellular ligand-binding receptor | ||||||
Keywords | SIGNALING PROTEIN / Solute Binding Protein / Tandem PAS sensor / ketoleucine / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Leucine-binding protein domain / Periplasmic binding protein / Periplasmic binding protein-like I / metal ion binding / ACETIC ACID / 2-OXO-4-METHYLPENTANOIC ACID / 6-AMINOPYRIMIDIN-2(1H)-ONE / Extracellular ligand-binding receptor Function and homology information | ||||||
Biological species | Desulfohalobium retbaense DSM 5692 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Cuff, M. / Wu, R. / Endres, M. / Pokkuluri, P.R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To Be Published Title: A novel extracellular ligand receptor Authors: Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ere.cif.gz | 221 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ere.ent.gz | 182.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ere.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/5ere ftp://data.pdbj.org/pub/pdb/validation_reports/er/5ere | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 62640.719 Da / Num. of mol.: 1 / Fragment: unp residues 32-599 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfohalobium retbaense DSM 5692 (bacteria) Strain: DSM 5692 / Gene: Dret_0059 / Production host: Escherichia coli (E. coli) / References: UniProt: C8WZ86 |
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-Non-polymers , 7 types, 230 molecules
#2: Chemical | ChemComp-COI / | ||
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#3: Chemical | ChemComp-CYT / | ||
#4: Chemical | ChemComp-ACY / | ||
#5: Chemical | ChemComp-CA / | ||
#6: Chemical | ChemComp-GOL / | ||
#7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.35 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MCSG-4 #95 (H11): 0.2M calcium acetate, 0.1 M Hepes pH 7.5, 10% PEG8000, 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 53557 / % possible obs: 99.9 % / Redundancy: 20 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 43.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→33.187 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33.187 Å
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Refine LS restraints |
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LS refinement shell |
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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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