+Open data
-Basic information
Entry | Database: PDB / ID: 1n3x | ||||||
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Title | Ligand-free High-Affinity Maltose-Binding Protein | ||||||
Components | Maltose-binding periplasmic protein | ||||||
Keywords | SUGAR BINDING PROTEIN / Engineered mutant / MBPdel-unliganded / MBPdel / MBP / High-Affinity / conformational engineering / Maltose-Binding protein | ||||||
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: 2.5 Å | ||||||
Authors | Telmer, P.G. / Shilton, B.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Insights into the Conformational Equilibria of Maltose-binding Protein by Analysis of High Affinity Mutants. 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 | 1n3x.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n3x.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 1n3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/1n3x ftp://data.pdbj.org/pub/pdb/validation_reports/n3/1n3x | HTTPS FTP |
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-Related structure data
Related structure data | 1n3wC 1nl5C 1pebC 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: 40217.590 Da / Num. of mol.: 1 / Mutation: Deletion of residues 172,173,175,176. Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MALE / Plasmid: pLH1del / Production host: Escherichia coli (E. coli) / Strain (production host): HS3309 / References: UniProt: P02928, UniProt: P0AEX9*PLUS |
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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: 2.26 Å3/Da / Density % sol: 45.06 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5479 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 30, 2001 / Details: other |
Radiation | Monochromator: Graded Mulitlayer (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5479 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→23.79 Å / Num. obs: 15189 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.48→2.59 Å / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 9.5 / % possible all: 97.8 |
Reflection | *PLUS Num. obs: 12399 / % possible obs: 98 % / Redundancy: 7.6 % |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OMP Resolution: 2.5→23.79 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 8640970.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.4075 Å2 / ksol: 0.359784 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→23.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 23.8 Å / Num. reflection obs: 12151 / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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