+Open data
-Basic information
Entry | Database: PDB / ID: 1sg2 | ||||||
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Title | Crystal structure of the periplasmic chaperone Skp | ||||||
Components | Seventeen Kilodalton Protein | ||||||
Keywords | CHAPERONE / protein folding / outer membrane protein / molecular dipole / hydrophobic surface | ||||||
Function / homology | Function and homology information protein insertion into membrane from inner side / Gram-negative-bacterium-type cell outer membrane assembly / protein maturation by protein folding / chaperone-mediated protein folding / lipopolysaccharide binding / unfolded protein binding / protein folding / outer membrane-bounded periplasmic space / protein stabilization / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å | ||||||
Authors | Korndorfer, I.P. / Dommel, M.K. / Skerra, A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structure of the periplasmic chaperone Skp suggests functional similarity with cytosolic chaperones despite differing architecture. Authors: Korndorfer, I.P. / Dommel, M.K. / Skerra, A. #1: Journal: To be Published Title: The periplasmic E. coli chaperone Skp is a trimer in solution: biophysical and preliminary crystallographic characterization Authors: Schlapschy, M. / Dommel, M.K. / Hadian, K. / Fogarasi, M. / Korndoerfer, I.P. / Skerra, A. | ||||||
History |
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Remark 999 | SEQUENCE ASWSHPQFEK IS THE SEQUENCE OF THE N-TERMINAL STREP-TAGII, WHICH THE AUTHORS USED TO PURIFY ...SEQUENCE ASWSHPQFEK IS THE SEQUENCE OF THE N-TERMINAL STREP-TAGII, WHICH THE AUTHORS USED TO PURIFY THE PROTEIN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sg2.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sg2.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 1sg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sg2_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 1sg2_full_validation.pdf.gz | 468.7 KB | Display | |
Data in XML | 1sg2_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1sg2_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/1sg2 ftp://data.pdbj.org/pub/pdb/validation_reports/sg/1sg2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is the trimer in the crystallographic asymmetric unit. |
-Components
#1: Protein | Mass: 17044.240 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: HLPA, SKP, OMPH, B0178, C0215, Z0190, ECS0180, SF0168, S0171 Plasmid: pASK75-IBA4-Skp / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P0AEU7 #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: 3.6 Å3/Da / Density % sol: 65.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 34.5% (v/v) ethanol, 7% (w/v) polyethylene glycol 1000, 50 mM Na-phosphate, 50 mM Na-citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.93221 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 6, 2003 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93221 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 63722 / Num. obs: 31346 / % possible obs: 94.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.059 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 17.7 / Num. unique all: 4407 / Rsym value: 0.325 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.878 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.244 / ESU R Free: 0.227 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.951 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / 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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