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Yorodumi- PDB-2ia4: Crystal structure of Novel amino acid binding protein from Shigel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ia4 | ||||||
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Title | Crystal structure of Novel amino acid binding protein from Shigella flexneri | ||||||
Components | Putative periplasmic binding transport protein | ||||||
Keywords | PROTEIN TRANSPORT / beta-alpha mixture | ||||||
Function / homology | Function and homology information Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Shigella flexneri 2a str. 301 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Fan, C.P. / Wang, D.C. | ||||||
Citation | Journal: To be Published Title: Structural and functional study of novel amino acid binding protein from Shigella flexneri Authors: Fan, C.P. / Wang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ia4.cif.gz | 130.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ia4.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ia4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/2ia4 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/2ia4 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32531.609 Da / Num. of mol.: 2 / Fragment: residues 1-279 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 2a str. 301 (bacteria) Species: Shigella flexneri / Strain: 2a 301 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q83S74, UniProt: A0A0H2UXX1*PLUS #2: Chemical | #3: Chemical | #4: 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: 1.99 Å3/Da / Density % sol: 38.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: trimethylamine N-oxide dihydrate, Polyethylene Glycol, Monomethyl ether 2000, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9500, 0.9794, 0.9799 | ||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2005 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. all: 160587 / Num. obs: 154166 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 28.7 | ||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 4 / Num. unique all: 8038 / Rsym value: 0.286 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→33.36 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 261723.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.9813 Å2 / ksol: 0.338119 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→33.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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