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Yorodumi- PDB-2hng: The Crystal Structure of Protein of Unknown Function SP1558 from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hng | ||||||
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Title | The Crystal Structure of Protein of Unknown Function SP1558 from Streptococcus pneumoniae | ||||||
Components | Hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Protein of unknown function DUF1149 / Protein of unknown function (DUF1149) / Bacterial Protein-export protein SecB / SecB-like / SecB-like superfamily / Roll / Alpha Beta / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å | ||||||
Authors | Kim, Y. / Zhang, D. / Zhou, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published / Year: 2006 Title: The Crystal Structure of Hypothetical Protein SP_1558 from Streptococcus pneumoniae Authors: Kim, Y. / Zhang, D. / Zhou, M. / 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 | 2hng.cif.gz | 42.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hng.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 2hng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hng_validation.pdf.gz | 419.1 KB | Display | wwPDB validaton report |
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Full document | 2hng_full_validation.pdf.gz | 420.3 KB | Display | |
Data in XML | 2hng_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 2hng_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/2hng ftp://data.pdbj.org/pub/pdb/validation_reports/hn/2hng | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14837.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1558 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q97PP5, UniProt: A0A0H2UQV3*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.94 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Calcium chloride, 0.1M Bis-Tris pH 6.5, 45% MPD, 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-ID / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2006 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→43.03 Å / Num. all: 17399 / Num. obs: 16724 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1283 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.63→43.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.217 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.119 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.122 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→43.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.672 Å / Total num. of bins used: 20
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