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Yorodumi- PDB-3kn3: Crystal Structure of LysR Substrate Binding Domain (25-263) of Pu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kn3 | ||||||
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Title | Crystal Structure of LysR Substrate Binding Domain (25-263) of Putative Periplasmic Protein from Wolinella succinogenes | ||||||
Components | PUTATIVE PERIPLASMIC PROTEIN | ||||||
Keywords | TRANSCRIPTION / alpha-beta structure / periplasmic binding protein fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Wolinella succinogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.412 Å | ||||||
Authors | Kim, Y. / Volkart, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of LysR Substrate Binding Domain from Wolinella succinogenes Authors: Kim, Y. / Volkart, L. / Bearden, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kn3.cif.gz | 290.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kn3.ent.gz | 246.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kn3_validation.pdf.gz | 780.2 KB | Display | wwPDB validaton report |
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Full document | 3kn3_full_validation.pdf.gz | 795.8 KB | Display | |
Data in XML | 3kn3_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 3kn3_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/3kn3 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/3kn3 | HTTPS FTP |
-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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 27302.154 Da / Num. of mol.: 3 / Fragment: LysR Substrate Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wolinella succinogenes (bacteria) / Strain: DSMZ 1740 / Gene: WS1370 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: Q7M8V9 |
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-Non-polymers , 5 types, 277 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ACY / | #4: Chemical | ChemComp-GSH / | #5: Chemical | ChemComp-CIT / | #6: 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: 2.37 Å3/Da / Density % sol: 48.06 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 0.1 M Citric acid pH 3.5, 25 % w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 2, 2009 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→34.53 Å / Num. all: 29443 / Num. obs: 29443 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 44.5 Å2 / Rsym value: 0.118 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.41→2.45 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 1362 / Rsym value: 0.401 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.412→34.527 Å / SU ML: 0.34 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.097 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.412→34.527 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain C |