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- PDB-2pv1: Crystallographic Structure of SurA first peptidyl-prolyl isomeras... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pv1 | ||||||
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Title | Crystallographic Structure of SurA first peptidyl-prolyl isomerase domain complexed with peptide WEYIPNV | ||||||
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![]() | ISOMERASE / Survival protein A / Peptidyl-prolyl cis-trans isomerase domain / Complex | ||||||
Function / homology | ![]() maintenance of stationary phase / maintenance of unfolded protein / Gram-negative-bacterium-type cell outer membrane assembly / chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / peptide binding / unfolded protein binding / protein folding / transferase activity ...maintenance of stationary phase / maintenance of unfolded protein / Gram-negative-bacterium-type cell outer membrane assembly / chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / peptide binding / unfolded protein binding / protein folding / transferase activity / outer membrane-bounded periplasmic space / protein stabilization Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, X. / McKay, D.B. | ||||||
![]() | ![]() Title: The Periplasmic Bacterial Molecular Chaperone SurA Adapts its Structure to Bind Peptides in Different Conformations to Assert a Sequence Preference for Aromatic Residues. Authors: Xu, X. / Wang, S. / Hu, Y.X. / McKay, D.B. #1: ![]() Title: Crystallographic structure of SurA, a molecular chaperone that facilitates folding of outer membrane porins Authors: Bitto, E. / McKay, D.B. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.6 KB | Display | ![]() |
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PDB format | ![]() | 23.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.2 KB | Display | ![]() |
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Full document | ![]() | 424.4 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pv2C ![]() 2pv3C ![]() 1m5yS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 10977.320 Da / Num. of mol.: 1 / Fragment: PpiC 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 920.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q2RHX9 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25~28% polyethylene glycol monomethylether 5000, 0.2 M ammonium sulfate, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→50 Å / Num. obs: 26586 / % possible obs: 98.4 % / Redundancy: 4.5 % / Rsym value: 0.034 / Χ2: 2.508 / Net I/σ(I): 39.7 |
Reflection shell | Resolution: 1.29→1.34 Å / Redundancy: 3.5 % / Num. unique all: 2504 / Rsym value: 0.126 / Χ2: 2.009 / % possible all: 93.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1M5Y Resolution: 1.3→41.05 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 44.38 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.142 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.3→41.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.38 Å / Rfactor Rfree error: 0.014
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Xplor file |
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