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Yorodumi- PDB-2pv3: Crystallographic Structure of SurA fragment lacking the second pe... -
+Open data
-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 | ||||||
Components |
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Keywords | ISOMERASE / Survival protein A / Peptidyl-prolyl cis-trans isomerase domain | ||||||
Function / homology | Function and homology information 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 / outer membrane-bounded periplasmic space / protein stabilization Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.39 Å | ||||||
Authors | Xu, X. / McKay, D.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 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: Journal: Structure / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pv3.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pv3.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 2pv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pv3_validation.pdf.gz | 444.5 KB | Display | wwPDB validaton report |
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Full document | 2pv3_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 2pv3_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 2pv3_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/2pv3 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/2pv3 | HTTPS FTP |
-Related structure data
Related structure data | 2pv1C 2pv2C 1m5yS S: Starting model for refinement C: citing same article (ref.) |
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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: 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.) Escherichia coli (E. coli) / Strain: K-12 EMG2 / Gene: surA / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0ABZ6, peptidylprolyl isomerase #2: Protein/peptide | | Mass: 1617.910 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD 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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