+Open data
-Basic information
Entry | Database: PDB / ID: 3zqb | ||||||
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Title | PrgI-SipD from Salmonella typhimurium | ||||||
Components | PROTEIN PRGI, CELL INVASION PROTEIN SIPD | ||||||
Keywords | CELL INVASION / TYPE III SECRETION / T3SS / TIP COMPLEX / HOST PATHOGEN INTERACTION / 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 ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 3zqb.cif.gz | 116.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zqb.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zqb ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zqb | HTTPS FTP |
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-Related structure data
Related structure data | 2ym0SC 2ym9C 3zqeC 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: (-0.6819, -0.6953, 0.227), Vector: |
-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.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) Strain: SL1344 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41784, UniProt: Q56026 #2: Chemical | #3: Water | ChemComp-HOH / | 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % / Description: NONE |
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Crystal grow | Details: PROTEIN WAS MIXED WITH SOLUTION CONTAINING 0.49 M NA H2PO4 MONOHYDRATE AND 0.91 M K2 HPO4, PH 6.9. |
-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: Jul 28, 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: 2.4→40 Å / Num. obs: 27970 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.47 |
Reflection shell | Resolution: 2.4→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.97 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YM0 Resolution: 2.4→32.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3356068.06 / 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: 52.8163 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→32.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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