+Open data
-Basic information
Entry | Database: PDB / ID: 7og8 | ||||||
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Title | Wild-type Hfq protein from Neisseria meningitidis | ||||||
Components | RNA-binding protein Hfq | ||||||
Keywords | RNA BINDING PROTEIN / sRNA / mRNA / annealing | ||||||
Function / homology | RNA-binding protein Hfq / Hfq protein / LSM domain superfamily / regulation of DNA-templated transcription / RNA binding / RNA-binding protein Hfq Function and homology information | ||||||
Biological species | Neisseria meningitidis serogroup C / serotype 2a | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Moche, M. / Karlsson, J. / Loh, E. | ||||||
Citation | Journal: To Be Published Title: Crystal structures of wild type, Q9A and R17A single mutant Hfq structures from Neisseria meningitidis Authors: Karlsson, J. / Moche, M. / Loh, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7og8.cif.gz | 28.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7og8.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 7og8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7og8_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 7og8_full_validation.pdf.gz | 428 KB | Display | |
Data in XML | 7og8_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 7og8_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/7og8 ftp://data.pdbj.org/pub/pdb/validation_reports/og/7og8 | HTTPS FTP |
-Related structure data
Related structure data | 7ogwC 7oh8C 4pnoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 7676.911 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup C / serotype 2a (strain ATCC 700532 / DSM 15464 / FAM18) (bacteria) Strain: ATCC 700532 / DSM 15464 / FAM18 / Gene: hfq, NMC0702 / Production host: Escherichia coli (E. coli) / References: UniProt: A1KT11 |
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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: 1.89 Å3/Da / Density % sol: 35.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: PEG3350, sodium nitrate, glycerol, bis-tris propane PH range: 6.1-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 19, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→30.27 Å / Num. obs: 11543 / % possible obs: 100 % / Redundancy: 18.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.027 / Rrim(I) all: 0.116 / Net I/σ(I): 13.7 / Num. measured all: 211386 / Scaling rejects: 1406 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PNO Resolution: 1.4→20.35 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / SU B: 1.56 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 56.97 Å2 / Biso mean: 14.642 Å2 / Biso min: 6.66 Å2
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Refinement step | Cycle: final / Resolution: 1.4→20.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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