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- PDB-3zqe: PrgI-SipD from Salmonella typhimurium in complex with deoxycholate -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zqe | ||||||
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Title | PrgI-SipD from Salmonella typhimurium in complex with deoxycholate | ||||||
![]() | PROTEIN PRGI, CELL INVASION PROTEIN SIPD | ||||||
![]() | CELL INVASION / CELL INVASION COMPLEX / TYPE III SECRETION / T3SS / TIP COMPLEX / HOST PATHOGEN INTERACTION / BACTERIAL PATHOGENESIS / BILE SALT | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lunelli, M. / Kolbe, M. | ||||||
![]() | ![]() Title: Crystal Structure of Prgi-Sipd: Insight Into a Secretion Competent State of the Type Three Secretion System Needle Tip and its Interaction with Host Ligands Authors: Lunelli, M. / Hurwitz, R. / Lambers, J. / Kolbe, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.6 KB | Display | ![]() |
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PDB format | ![]() | 89.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 750.6 KB | Display | ![]() |
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Full document | ![]() | 766.4 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ym0C ![]() 2ym9C ![]() 3zqbSC C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.6858, -0.6888, 0.235), Vector: |
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Components
#1: Protein | Mass: 33158.875 Da / Num. of mol.: 2 / Fragment: PRGI FUSED WITH SIPD RESIDUES 127-343 Source method: isolated from a genetically manipulated source Details: GGSGG LINK INSERTED BETWEEN PRGI AND SIPD Source: (gene. exp.) ![]() Strain: SL1344 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-DXC / ( | #4: Water | ChemComp-HOH / | Nonpolymer details | (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYC | Sequence details | RESIDUES GSH AT THE N-TERMINUS REMAINING AFTER HIS-TAG CLEAVAGE. GGSGG LINKER INSERTED BETWEEN PRGI ...RESIDUES GSH AT THE N-TERMINUS REMAINING AFTER HIS-TAG CLEAVAGE. GGSGG LINKER INSERTED BETWEEN PRGI AND SIPD127-343. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % / Description: NONE |
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Crystal grow | Details: PROTEIN WAS MIXED WITH SOLUTION CONTAINING 0.026 M NAH2PO4 AND 1.26 M K2HPO4. OBTAINED CRYSTALS WERE SOAKED FOR 72 HOURS IN SAME SOLUTION CONTAINING 0.01 M DEOXYCHOLATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→40 Å / Num. obs: 34906 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.02 |
Reflection shell | Resolution: 2.19→2.26 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.73 / % possible all: 84.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZQB Resolution: 2.19→36.48 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3170360.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: BULK SOLVENT MODEL USED. THE CHAINS WERE RENUMBERED TO BE CONSISTENT WITH NUMBERING OF THE BIOLOGICALLY ACTIVE MOLECULES FOR WHICH THERE ARE EXISTING PDB AND UNIPROT ENTRIES.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.4442 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.19→36.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.19→2.33 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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