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Yorodumi- PDB-2ior: Crystal Structure of the N-terminal Domain of HtpG, the Escherich... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ior | ||||||
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Title | Crystal Structure of the N-terminal Domain of HtpG, the Escherichia coli Hsp90, Bound to ADP | ||||||
Components | Chaperone protein htpG | ||||||
Keywords | CHAPERONE / Heat Shock Protein / Hsp90 | ||||||
Function / homology | Function and homology information FtsZ-dependent cytokinesis / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / response to heat / protein-folding chaperone binding / DNA damage response / ATP hydrolysis activity / protein homodimerization activity ...FtsZ-dependent cytokinesis / protein folding chaperone / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / response to heat / protein-folding chaperone binding / DNA damage response / ATP hydrolysis activity / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Shiau, A.K. / Harris, S.F. / Agard, D.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: Structural Analysis of E. coli hsp90 reveals dramatic nucleotide-dependent conformational rearrangements. Authors: Shiau, A.K. / Harris, S.F. / Southworth, D.R. / Agard, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ior.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ior.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ior.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/2ior ftp://data.pdbj.org/pub/pdb/validation_reports/io/2ior | HTTPS FTP |
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-Related structure data
Related structure data | 2gq0C 2iopC 2ioqC 1byqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26397.396 Da / Num. of mol.: 1 / Fragment: N-terminal Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: htpG / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Z3 | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2-12% PEG4000, 0.5M 1,6-hexanediol, 0.1M NaOAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2003 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→55.9 Å / Num. all: 29672 / Num. obs: 29467 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.65→1.69 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3 / Num. unique all: 1851 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BYQ Resolution: 1.65→55.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.53 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→55.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.692 Å / Total num. of bins used: 20
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