+Open data
-Basic information
Entry | Database: PDB / ID: 2ym0 | |||||||||
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Title | Truncated SipD from Salmonella typhimurium | |||||||||
Components | CELL INVASION PROTEIN SIPD | |||||||||
Keywords | CELL INVASION / TYPE 3 SECRETION / T3SS / NEEDLE TIP PROTEIN / HOST PATHOGEN INTERACTION / BACTERIAL PATHOGENESIS / TIP COMPLEX | |||||||||
Function / homology | IpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / extracellular region / Mainly Alpha / Cell invasion protein SipD Function and homology information | |||||||||
Biological species | SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Lunelli, M. / Kolbe, M. | |||||||||
Citation | Journal: PLoS Pathog. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ym0.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ym0.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ym0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/2ym0 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/2ym0 | HTTPS FTP |
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-Related structure data
Related structure data | 2ym9C 3zqbC 3zqeC 2j0nS 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: (-0.975, -0.2222, -0.002823), Vector: |
-Components
#1: Protein | Mass: 25499.508 Da / Num. of mol.: 2 / Fragment: RESIDUES 132-343 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) Strain: SL1344 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56026 #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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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: 3.04 Å3/Da / Density % sol: 59.6 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: PROTEIN WAS MIXED WITH EQUAL VOLUME OF SOLUTION 0.1 M MES PH 6.5 AND 12% (W/V) PEG 20000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2009 / 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: 3→40 Å / Num. obs: 12938 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 63.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.77 |
Reflection shell | Resolution: 3→3.15 Å / Redundancy: 5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.42 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J0N Resolution: 3→37.21 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2346361.93 / 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.41 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→37.21 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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