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Yorodumi- PDB-7ofz: Nontypeable Haemophillus influenzae SapA in complex with double s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ofz | ||||||
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Title | Nontypeable Haemophillus influenzae SapA in complex with double stranded RNA | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / NTHi / RNA binding / peptide binding / substrate binding protein | ||||||
Function / homology | Function and homology information peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.62 Å | ||||||
Authors | Lukacik, P. / Owen, C.D. / Nettleship, J.E. / Bird, L.E. / Owens, R.J. / Walsh, M.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Plos One / Year: 2021 Title: The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif. Authors: Lukacik, P. / Owen, C.D. / Harris, G. / Bolla, J.R. / Picaud, S. / Alibay, I. / Nettleship, J.E. / Bird, L.E. / Owens, R.J. / Biggin, P.C. / Filippakopoulos, P. / Robinson, C.V. / Walsh, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ofz.cif.gz | 133.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ofz.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ofz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ofz_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
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Full document | 7ofz_full_validation.pdf.gz | 432.1 KB | Display | |
Data in XML | 7ofz_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 7ofz_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/7ofz ftp://data.pdbj.org/pub/pdb/validation_reports/of/7ofz | HTTPS FTP |
-Related structure data
Related structure data | 7ofwC 7og0C 3m8uS 6him 6hj1 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60102.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (strain 86-028NP) (bacteria) Strain: 86-028NP / Gene: sapA, NTHI1401 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QL73 |
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#2: RNA chain | Mass: 6113.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: This RNA sequence is the best interpretation of the electron density Source: (natural) Escherichia coli (E. coli) |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 22% (w/v) PEG 3350, 0.25 M NaBr, 0.1 M Bis-Tris Propane pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.62→72.2 Å / Num. obs: 19346 / % possible obs: 95.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 89.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.129 / Χ2: 0.966 / Net I/σ(I): 13.08 / Num. measured all: 145122 / Scaling rejects: 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M8U Resolution: 2.62→72.2 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.892 / SU R Cruickshank DPI: 1.138 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.033 / SU Rfree Blow DPI: 0.34 / SU Rfree Cruickshank DPI: 0.339
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Displacement parameters | Biso max: 175.85 Å2 / Biso mean: 69.57 Å2 / Biso min: 32.96 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.62→72.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.62→2.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 47
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