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Yorodumi- PDB-1tm2: Crystal Structure of the apo form of the Salmonella typhimurium A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tm2 | ||||||
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Title | Crystal Structure of the apo form of the Salmonella typhimurium AI-2 receptor LsrB | ||||||
Components | sugar transport protein | ||||||
Keywords | SIGNALING PROTEIN / PERIPLASMIC BINDING PROTEIN | ||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / carbohydrate binding Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Miller, S.T. / Xavier, K.B. / Campagna, S.R. / Taga, M.E. / Semmelhack, M.F. / Bassler, B.L. / Hughson, F.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Salmonella typhimurium Recognizes a Chemically Distinct Form of the Bacterial Quorum-Sensing Signal AI-2 Authors: Miller, S.T. / Xavier, K.B. / Campagna, S.R. / Taga, M.E. / Semmelhack, M.F. / Bassler, B.L. / Hughson, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tm2.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tm2.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1tm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tm2_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 1tm2_full_validation.pdf.gz | 429.3 KB | Display | |
Data in XML | 1tm2_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1tm2_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/1tm2 ftp://data.pdbj.org/pub/pdb/validation_reports/tm/1tm2 | HTTPS FTP |
-Related 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: 34250.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: LsrB / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8Z2X8, UniProt: Q8ZKQ1*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.9→27.13 Å / Num. all: 25812 / Num. obs: 25812 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→2.02 Å / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→27.13 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→27.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013
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