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- PDB-2pv3: Crystallographic Structure of SurA fragment lacking the second pe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pv3 | ||||||
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Title | Crystallographic Structure of SurA fragment lacking the second peptidyl-prolyl isomerase domain complexed with peptide NFTLKFWDIFRK | ||||||
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Function / homology | ![]() maintenance of stationary phase / maintenance of unfolded protein / Gram-negative-bacterium-type cell outer membrane assembly / chaperone-mediated protein folding / ![]() ![]() ![]() ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.1 KB | Display | ![]() |
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PDB format | ![]() | 93 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2pv1C ![]() 2pv2C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 33221.621 Da / Num. of mol.: 2 Fragment: Survivial protein A fragment from which the second peptidyl-prolyl isomerase domain has been deleted Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | | ![]() Mass: 1617.910 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.4~1.8M sodium chloride, 0.1M potassium dihydrogen phosphate, 0.1 M sodium dihydrogen phosphate, 0.1M MES buffer, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 21, 2006 | ||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.39→50 Å / Num. obs: 33486 / % possible obs: 99.1 % / Redundancy: 4.2 % / Rsym value: 0.074 / Net I/σ(I): 17.5 | ||||||||||||||||||
Reflection shell | Resolution: 3.39→3.52 Å / Redundancy: 3.5 % / Num. unique all: 3326 / Rsym value: 0.422 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1M5Y Resolution: 3.39→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.908 / SU B: 22.754 / SU ML: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.501 / ESU R Free: 0.396 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 171.417 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.39→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.39→3.478 Å / Total num. of bins used: 20
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