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Yorodumi- PDB-1ziu: Crystal Structure of nickel-bound engineered Maltose Binding Protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ziu | ||||||
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Title | Crystal Structure of nickel-bound engineered Maltose Binding Protein | ||||||
Components | Maltose-binding periplasmic protein | ||||||
Keywords | SUGAR BINDING / METAL BINDING PROTEIN / Maltose binding protein / zinc biosensor / metal binding mutant / ABC transporters / protein engineering | ||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Telmer, P.G. / Shilton, B.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structural studies of an engineered zinc biosensor reveal an unanticipated mode of zinc binding. Authors: Telmer, P.G. / Shilton, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ziu.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ziu.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ziu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/1ziu ftp://data.pdbj.org/pub/pdb/validation_reports/zi/1ziu | HTTPS FTP |
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-Related structure data
Related structure data | 1zjlC 1zkbC 1zmgC 1ompS 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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Unit cell |
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-Components
#1: Protein | Mass: 40712.098 Da / Num. of mol.: 1 / Fragment: residues 27-396 / Mutation: A63H, R66H, E111M, Y155E, W340E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE / Plasmid: pLH1 / Production host: Escherichia coli (E. coli) / Strain (production host): HS3309 / References: UniProt: P02928, UniProt: P0AEX9*PLUS | ||
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#2: Chemical | #3: 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: 2.132 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 2000 MME, sodium acetate, nickel chloride, Tris-HCl, sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 10, 2005 / Details: osmic mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 24838 / Num. obs: 24397 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.057 / Χ2: 0.51 |
Reflection shell | Resolution: 2→2.07 Å / % possible obs: 94.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.192 / Num. measured obs: 2090 / Χ2: 0.648 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1OMP Resolution: 2→38.08 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 34.1686 Å2 / ksol: 0.356139 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.43 Å2 / Biso mean: 15.52 Å2 / Biso min: 4.67 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→38.08 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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