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Yorodumi- PDB-2x4h: Crystal Structure of the hypothetical protein SSo2273 from Sulfol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x4h | ||||||
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Title | Crystal Structure of the hypothetical protein SSo2273 from Sulfolobus solfataricus | ||||||
Components | HYPOTHETICAL PROTEIN SSO2273Hypothesis | ||||||
Keywords | TRANSCRIPTION | ||||||
Function / homology | Function and homology information transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding Similarity search - Function | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
Citation | Journal: J.Struct.Funct.Genomics / Year: 2010 Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x4h.cif.gz | 222.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x4h.ent.gz | 193.2 KB | Display | PDB format |
PDBx/mmJSON format | 2x4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/2x4h ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x4h | HTTPS FTP |
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-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 15958.334 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97WF3 #2: Chemical | ChemComp-ZN / #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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: OFFLINE FUJI PLATE. |
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Crystal grow | pH: 7 Details: 5.6%-6.8% PEG 1000, 80MM ZN ACETATE AND 0.1M MES PH7. THE CRYSTALS WERE CRYOPROTECTED BY ADDITION OF 25% PEG 400. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6 |
Detector | Type: FUJIFILM / Detector: IMAGE PLATE / Date: Mar 27, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→28.89 Å / Num. obs: 30005 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.8 / % possible all: 98.5 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.3→28.89 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.785 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES ONE TO NINE ARE DISORDERED IN CHAINS A AND D AND RESIDUES ONE TO EIGHT ARE DISORDERED IN CHAINS B AND C. ATOM RECORD CONTAINS SUM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES ONE TO NINE ARE DISORDERED IN CHAINS A AND D AND RESIDUES ONE TO EIGHT ARE DISORDERED IN CHAINS B AND C. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.417 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→28.89 Å
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