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Yorodumi- PDB-3mw6: Crystal structure of NMB1681 from Neisseria meningitidis MC58, a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mw6 | |||||||||
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Title | Crystal structure of NMB1681 from Neisseria meningitidis MC58, a FinO-like RNA chaperone | |||||||||
Components | uncharacterized protein NMB1681 | |||||||||
Keywords | structural genomics / unknown function / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG | |||||||||
Function / homology | Fertility Inhibition Protein O; Chain: A; Domain 1 / ProQ/FinO domain / ProQ/FinO domain superfamily / ProQ/FINO family / ProQ/FinO domain / ProQ/FINO family / Orthogonal Bundle / Mainly Alpha / ProQ/FinO domain-containing protein Function and homology information | |||||||||
Biological species | Neisseria meningitidis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.209 Å | |||||||||
Authors | Tan, K. / Zhou, M. / Duggan, E. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Citation | Journal: Rna Biol. / Year: 2010 Title: N. meningitidis 1681 is a member of the FinO family of RNA chaperones. Authors: Chaulk, S. / Lu, J. / Tan, K. / Arthur, D.C. / Edwards, R.A. / Frost, L.S. / Joachimiak, A. / Glover, J.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mw6.cif.gz | 281 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mw6.ent.gz | 238.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mw6_validation.pdf.gz | 486.4 KB | Display | wwPDB validaton report |
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Full document | 3mw6_full_validation.pdf.gz | 499.2 KB | Display | |
Data in XML | 3mw6_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 3mw6_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/3mw6 ftp://data.pdbj.org/pub/pdb/validation_reports/mw/3mw6 | 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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4 |
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Unit cell |
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Details | Experimentally unknown. Possibly, the chains A and B, C and D, E and F form dimers respectively. |
-Components
#1: Protein | Mass: 15933.576 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB1681 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JY98 #2: Chemical | ChemComp-GOL / | #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: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100MM BIS-TRIS, 170MM MGCL2, 21% PEG3350, pH 6.5, 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: 0.97932 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2001 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→109 Å / Num. obs: 96019 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1.92 / Num. unique all: 2736 / % possible all: 79.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.209→42.889 Å / SU ML: 0.33 / σ(F): 1.89 / σ(I): 0 / 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 / Bsol: 53.951 Å2 / ksol: 0.353 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.209→42.889 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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