+Open data
-Basic information
Entry | Database: PDB / ID: 1dj8 | ||||||
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Title | CRYSTAL STRUCTURE OF E. COLI PERIPLASMIC PROTEIN HDEA | ||||||
Components | PROTEIN HNS-DEPENDENT EXPRESSION A | ||||||
Keywords | STRUCTURAL PROTEIN / ALPHA HELICAL | ||||||
Function / homology | Function and homology information cellular stress response to acidic pH / cellular response to acidic pH / chaperone-mediated protein folding / protein folding chaperone / unfolded protein binding / outer membrane-bounded periplasmic space / protein-folding chaperone binding / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Gajiwala, K.S. / Burley, S.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria. Authors: Gajiwala, K.S. / Burley, S.K. #1: Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal Structure of Escherichia coli HdeA Authors: Yang, F. / Gustafson, K.R. / Boyd, M.R. / Wlodawer, A. #2: Journal: Electrophoresis / Year: 1997 Title: Comparing the Predicted and Observed Properties of Proteins Encoded in the Genome of Escherichia coli K-12 Authors: Link, A.J. / Robinson, K. / Church, G.H. #3: Journal: Mol.Microbiol. / Year: 1996 Title: Identification of Sigma S-Dependent Genes Associated with the Stationary-Phase Acid-Resistance Phenotype of Shigella flexneri Authors: Waterman, S.R. / Small, P.L. #4: Journal: Biochem.Biophys.Res.Commun. / Year: 1996 Title: Evidence for GroES Acting as Transcriptional Regulator Authors: Legname, G. / Buono, P. / Fossati, G. / Monzini, N. / Mascagni, P. / Modena, D. / Marcucci, F. #5: Journal: Mol.Microbiol. / Year: 1997 Title: H-NS: a Modulator of Environmentally Regulated Gene Expression Authors: Atlung, T. / Ingmer, H. | ||||||
History |
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Remark 99 | Author sent a new reflection file to supercede the initially released SF file in December, 1999. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dj8.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dj8.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/1dj8 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/1dj8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 9752.882 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: PERIPLASM / References: UniProt: P26604, UniProt: P0AES9*PLUS #2: 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: 2.18 Å3/Da / Density % sol: 43.57 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 4 Details: PEG1500, SODIUM ACETATE, pH 4, VAPOR DIFFUSION, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: OTHER / Detector: CCD / Date: Dec 5, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 33169 / Num. obs: 32222 / % possible obs: 97.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 12 / Redundancy: 8 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.123 / % possible all: 97.7 |
Reflection shell | *PLUS % possible obs: 97.7 % |
-Processing
Software |
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Refinement | Resolution: 2→15 Å / σ(F): 3 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.246 |