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Yorodumi- PDB-3d37: The crystal structure of the tail protein from Neisseria meningit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d37 | ||||||
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Title | The crystal structure of the tail protein from Neisseria meningitidis MC58 | ||||||
Components | Tail protein, 43 kDa | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / tail protein / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information Baseplate protein-like domain - beta roll fold / Baseplate protein-like domains - 2 layer sandwich fold / Baseplate-like, two-layer sandwich fold / Baseplate protein GpP / Phage tail proteins - horseshoe like beta roll fold / Baseplate protein-like domains / Phage tail protein beta-alpha-beta fold / Phage tail proteins - 2 layer sandwich fold / 3-Layer(bab) Sandwich / Roll ...Baseplate protein-like domain - beta roll fold / Baseplate protein-like domains - 2 layer sandwich fold / Baseplate-like, two-layer sandwich fold / Baseplate protein GpP / Phage tail proteins - horseshoe like beta roll fold / Baseplate protein-like domains / Phage tail protein beta-alpha-beta fold / Phage tail proteins - 2 layer sandwich fold / 3-Layer(bab) Sandwich / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Neisseria meningitidis MC58 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Zhang, R. / Li, H. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the tail protein from Neisseria meningitidis MC58. Authors: Zhang, R. / Li, H. / Bargassa, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d37.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d37.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 3d37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d37_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 3d37_full_validation.pdf.gz | 462.2 KB | Display | |
Data in XML | 3d37_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 3d37_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/3d37 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/3d37 | 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
#1: Protein | Mass: 42126.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Strain: MC58 / Serogroup B / Gene: GI:7226348, NMB1110 / Plasmid: pDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JZC8 #2: Chemical | ChemComp-CL / #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: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2M Potassium iodide, 20% PEG 3350, 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: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2006 / Details: Mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→97.13 Å / Num. all: 48038 / Num. obs: 47918 / % possible obs: 99.75 % / Observed criterion σ(I): 2 / Redundancy: 28.5 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 38.89 |
Reflection shell | Resolution: 2.1→2.155 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.39 / Num. unique all: 3705 / % possible all: 99.57 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→97.13 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.241 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.214 / ESU R Free: 0.197 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 33.105 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→97.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -22.636 Å / Origin y: 53.169 Å / Origin z: 97.926 Å
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Refinement TLS group |
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