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Yorodumi- PDB-5e7u: MBP-MamC loop structure, a magnetite biomineralizing protein from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e7u | |||||||||
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Title | MBP-MamC loop structure, a magnetite biomineralizing protein from Magnetospirillium magneticum AMB-1 | |||||||||
Components | Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein | |||||||||
Keywords | Magnetite binding protein / Magnetite binding / mineralization / MBP / transport protein | |||||||||
Function / homology | Function and homology information magnetosome membrane / detection of maltose stimulus / maltose transport complex / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...magnetosome membrane / detection of maltose stimulus / maltose transport complex / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Magnetospirillum magneticum AMB-1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Nudelman, H. / Zarivach, R. | |||||||||
Citation | Journal: To Be Published Title: MBP-MamC loop structure, a magnetite biomineralizing protein from Magnetospirillium magneticum AMB-1 Authors: Nudelman, H. / Zarivach, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e7u.cif.gz | 160.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e7u.ent.gz | 125.4 KB | Display | PDB format |
PDBx/mmJSON format | 5e7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e7u_validation.pdf.gz | 807.8 KB | Display | wwPDB validaton report |
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Full document | 5e7u_full_validation.pdf.gz | 811.6 KB | Display | |
Data in XML | 5e7u_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 5e7u_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/5e7u ftp://data.pdbj.org/pub/pdb/validation_reports/e7/5e7u | HTTPS FTP |
-Related structure data
Related structure data | 3puzS 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: 45190.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Magnetospirillum magneticum AMB-1 (bacteria) Gene: malE, Z5632, ECs5017, mms13, amb0951 / Production host: Escherichia coli (E. coli) References: UniProt: P0AEY0, UniProt: Q2W8S0, UniProt: P0AEX9*PLUS | ||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate , 2 M Ammonium sulfate / PH range: 3.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→63.52 Å / Num. obs: 11938 / % possible obs: 95.23 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 24.64 |
Reflection shell | Redundancy: 8.3 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 4.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PUZ Resolution: 2.8→63.52 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.827 / SU B: 49.523 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.074 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→63.52 Å
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Refine LS restraints |
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