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Yorodumi- PDB-1y9t: Crystal structure of a type III secretion system protein complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y9t | ||||||
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Title | Crystal structure of a type III secretion system protein complexed with the lipid, 1-monohexanoyl-2-hydroxy-sn-glycero-3-phosphate | ||||||
Components | Lipoprotein mxiM | ||||||
Keywords | LIPID BINDING PROTEIN / MIXED ALPHA/BETA / CRACKED B-BARREL FOLD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.87 Å | ||||||
Authors | Lario, P.I. / Strynadka, N.C. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Structure and biochemical analysis of a secretin pilot protein. Authors: Lario, P.I. / Pfuetzner, R.A. / Frey, E.A. / Creagh, L. / Haynes, C. / Maurelli, A.T. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y9t.cif.gz | 38.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y9t.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 1y9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y9t_validation.pdf.gz | 653.2 KB | Display | wwPDB validaton report |
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Full document | 1y9t_full_validation.pdf.gz | 654.1 KB | Display | |
Data in XML | 1y9t_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 1y9t_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/1y9t ftp://data.pdbj.org/pub/pdb/validation_reports/y9/1y9t | HTTPS FTP |
-Related structure data
Related structure data | 1y9lSC 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: 12903.888 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: mxiM / Plasmid: PET19B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A1X2 |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-HHG / ( |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: (NH3)2SO4 LiSO4 NaCHOCH3, 1-monohexanoyl-2-hydroxy-sn-glycero-3-phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→42.4 Å / Num. all: 9460 / Num. obs: 9460 / % possible obs: 96.37 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 32.5 Å2 / Rsym value: 0.027 / Net I/σ(I): 34 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 912 / Rsym value: 0.22 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1Y9L Resolution: 1.87→42.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.486 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 33.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→42.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.919 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.6107 Å / Origin y: 42.2189 Å / Origin z: 2.9285 Å
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