+Open data
-Basic information
Entry | Database: PDB / ID: 1nl5 | |||||||||
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Title | Engineered High-affinity Maltose-Binding Protein | |||||||||
Components | Maltose-binding periplasmic protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / MBP / MALTOSE-BINDING PROTEIN / HIGH-AFFINITY MUTANT / Maltodextrin-Binding Protein | |||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / 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 Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 1nl5.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nl5.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nl5_validation.pdf.gz | 808 KB | Display | wwPDB validaton report |
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Full document | 1nl5_full_validation.pdf.gz | 814.1 KB | Display | |
Data in XML | 1nl5_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1nl5_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/1nl5 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/1nl5 | HTTPS FTP |
-Related structure data
Related structure data | 1n3wC 1n3xC 1pebC 1anfS 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: 40100.422 Da / Num. of mol.: 1 / Mutation: M321A Q325A, 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: pLH1-dm2 / Production host: Escherichia coli (E. coli) / Strain (production host): HS3309 / References: UniProt: P02928, UniProt: P0AEX9*PLUS |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Chemical | ChemComp-ZN / |
#4: 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: 2.6 Å3/Da / Density % sol: 52.37 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 3350, Zinc Chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.2 / 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: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 2002 / Details: Other |
Radiation | Monochromator: Graded Multilayer (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→60.8 Å / Num. all: 27867 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.047 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.19 / % possible all: 100 |
Reflection | *PLUS Num. all: 27825 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1ANF Resolution: 2.1→60.8 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 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: 65.2334 Å2 / ksol: 0.368216 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36 Å2
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Refine analyze | Luzzati coordinate error free: 0.4 Å / Luzzati sigma a free: 0.41 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→60.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 60.8 Å / Num. reflection obs: 27074 / Rfactor Rfree: 0.29 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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