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Yorodumi- PDB-3clq: Crystal structure of a conserved protein of unknown function from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3clq | ||||||
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Title | Crystal structure of a conserved protein of unknown function from Enterococcus faecalis V583 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC29596.3 / conserved protein of unknown function / Enterococcus faecalis V583 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information conserved protein of unknown function from Enterococcus faecalis V583 / v583 fold / v583 domain like / Enterococcus faecalis V583 fold / Enterococcus faecalis V583 domain / Protein of unknown function DUF1116 / Uncharacterised domain superfamily, YlbE / Protein of unknown function (DUF1116) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...conserved protein of unknown function from Enterococcus faecalis V583 / v583 fold / v583 domain like / Enterococcus faecalis V583 fold / Enterococcus faecalis V583 domain / Protein of unknown function DUF1116 / Uncharacterised domain superfamily, YlbE / Protein of unknown function (DUF1116) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Tan, K. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a conserved protein of unknown function from Enterococcus faecalis V583. Authors: Tan, K. / Duggan, E. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3clq.cif.gz | 310.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3clq.ent.gz | 267.1 KB | Display | PDB format |
PDBx/mmJSON format | 3clq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3clq_validation.pdf.gz | 477.7 KB | Display | wwPDB validaton report |
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Full document | 3clq_full_validation.pdf.gz | 531.3 KB | Display | |
Data in XML | 3clq_validation.xml.gz | 61.5 KB | Display | |
Data in CIF | 3clq_validation.cif.gz | 83.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/3clq ftp://data.pdbj.org/pub/pdb/validation_reports/cl/3clq | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. BASED ON THE CRYSTAL STRUCTURE, CHAINS A,B LIKELY FORM A DIMER, AND CHAINS C,D LIKELY FORM ANOTHER DIMER. |
-Components
#1: Protein | Mass: 45954.180 Da / Num. of mol.: 4 / Fragment: Residues 57-474 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_3011 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q82ZN9 #2: Chemical | ChemComp-PEG / #3: 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: 2.79 Å3/Da / Density % sol: 55.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M NaCl, 0.1M Tris-HCl, 25% w/v PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951, 0.97965 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2007 / Details: Mirrors | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→43.03 Å / Num. all: 62694 / Num. obs: 62694 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 22.9 | |||||||||
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 3 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 1.88 / Num. unique all: 3223 / % possible all: 54.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→43.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 23.244 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.579 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 55.801 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→43.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.566 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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