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Yorodumi- PDB-2x9c: Crystal structure of a soluble PrgI mutant from Salmonella Typhimurium -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x9c | ||||||
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Title | Crystal structure of a soluble PrgI mutant from Salmonella Typhimurium | ||||||
Components | PROTEIN PRGI | ||||||
Keywords | PROTEIN TRANSPORT / NEEDLE PROTOMER / BACTERIAL PATHOGENESIS | ||||||
Function / homology | Function and homology information type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | SALMONELLA TYPHIMURIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Poyraz, O. / Schmidt, H. / Seidel, K. / Delissen, F. / Ader, C. / Tenenboim, H. / Goosmann, C. / Laube, B. / Thuenemann, A.F. / Zychlinsky, A. ...Poyraz, O. / Schmidt, H. / Seidel, K. / Delissen, F. / Ader, C. / Tenenboim, H. / Goosmann, C. / Laube, B. / Thuenemann, A.F. / Zychlinsky, A. / Baldus, M. / Lange, A. / Griesinger, C. / Kolbe, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Protein Refolding is Required for Assembly of the Type Three Secretion Needle Authors: Poyraz, O. / Schmidt, H. / Seidel, K. / Delissen, F. / Ader, C. / Tenenboim, H. / Goosmann, C. / Laube, B. / Thuenemann, A.F. / Zychlinsky, A. / Baldus, M. / Lange, A. / Griesinger, C. / Kolbe, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x9c.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x9c.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 2x9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/2x9c ftp://data.pdbj.org/pub/pdb/validation_reports/x9/2x9c | HTTPS FTP |
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-Related structure data
Related structure data | 2kv7C 2ca5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9934, -0.09595, 0.06291), Vector: |
-Components
#1: Protein | Mass: 9091.037 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Strain: SL1344 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P41784 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, VAL 65 TO ALA ENGINEERED RESIDUE IN CHAIN A, VAL 67 TO ALA ...ENGINEERED | |
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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: 3.45 Å3/Da / Density % sol: 64.4 % Description: DATA DETWINNED USING CNS WITH TWIN FRACTION 0.18 AND TWIN OPERATOR K,H,-L |
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Crystal grow | Method: vapor diffusion, hanging drop Details: RESERVOIR SOLUTION 0.15 MM NAH2PO4. SAMPLE BUFFER 20 MM HEPES (PH 7.5) 50 MM NACL. HANGING DROP WITH 1 UL SAMPLE AND 1 UL RESERVOIR SOLUTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2007 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 11435 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 63.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.83 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.11 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CA5 Resolution: 2.45→38.13 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2660057.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: CHAIN A RESIDUES 1-18 AND 80 ARE DISORDERED. CHAIN B RESIDUES 1-17 ARE DISORDERED. N-TERMINAL RESIDUES GLY-SER-HIS REMAINING FROM THROMBIN CLEAVAGE SITE ARE DISORDERED IN CHAINS A AND B. THE ...Details: CHAIN A RESIDUES 1-18 AND 80 ARE DISORDERED. CHAIN B RESIDUES 1-17 ARE DISORDERED. N-TERMINAL RESIDUES GLY-SER-HIS REMAINING FROM THROMBIN CLEAVAGE SITE ARE DISORDERED IN CHAINS A AND B. THE STRUCTURE WAS REFINED AT LOWER RESOLUTION (2.45 A) THAN THE COLLECTED DATASET (2.25 A) BECAUSE OF THE POOR MERGING STATISTICS AT HIGH RESOLUTION.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 79.6715 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→38.13 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.071 / Total num. of bins used: 6
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Xplor file |
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