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Yorodumi- PDB-6wn5: 1.52 Angstrom Resolution Crystal Structure of Transcriptional Reg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wn5 | ||||||
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Title | 1.52 Angstrom Resolution Crystal Structure of Transcriptional Regulator HdfR from Klebsiella pneumoniae | ||||||
Components | Transcriptional regulator HdfR | ||||||
Keywords | TRANSCRIPTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Transcriptional Regulator HdfR | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Microbiol Resour Announc / Year: 2023 Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae. Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wn5.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wn5.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/6wn5 ftp://data.pdbj.org/pub/pdb/validation_reports/wn/6wn5 | HTTPS FTP |
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-Related structure data
Related structure data | 6dt3C 6duxC 6dvvC 6dxnC 6e85C 6nauC 6nbgC 6ndiC 6wn8C 6x1lC 7rjjC 7tl5C 7tzpC C: citing same article (ref.) |
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Similar structure data | |
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: 26702.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Gene: hdfR, B6R99_21715 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (DE)magic / References: UniProt: A0A657RSZ5, UniProt: W1HWH8*PLUS | ||||
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#2: Chemical | #3: 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: 1.92 Å3/Da / Density % sol: 36.1 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Protein: 7.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen (PACT, E10): 0.2 M Sodium/Potassium phosphate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2019 / Details: Be |
Radiation | Monochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→30 Å / Num. obs: 32133 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.019 / Rrim(I) all: 0.061 / Rsym value: 0.057 / Χ2: 1.466 / Net I/σ(I): 44.4 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1569 / CC1/2: 0.91 / CC star: 0.976 / Rpim(I) all: 0.263 / Rrim(I) all: 0.827 / Rsym value: 0.783 / Χ2: 0.999 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.52→29.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.973 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.077 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.3 Å2 / Biso mean: 26.801 Å2 / Biso min: 8.91 Å2
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Refinement step | Cycle: final / Resolution: 1.52→29.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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