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Yorodumi- PDB-1jvx: Maltodextrin-binding protein variant D207C/A301GS/P316C cross-lin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jvx | |||||||||
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Title | Maltodextrin-binding protein variant D207C/A301GS/P316C cross-linked in crystal | |||||||||
Components | maltodextrin-binding protein | |||||||||
Keywords | TRANSPORT PROTEIN / intermolecular / cross-link / disulfide | |||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate 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 Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Srinivasan, U. / Iyer, G.H. / Przybycien, T.A. / Samsonoff, W.A. / Bell, J.A. | |||||||||
Citation | Journal: Protein Eng. / Year: 2002 Title: Crystine: Fibrous Biomolecular Material from Protein Crystals Cross-linked in a Specific Geometry Authors: Srinivasan, U. / Iyer, G.H. / Przybycien, T.A. / Samsonoff, W.A. / Bell, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jvx.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jvx.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/1jvx ftp://data.pdbj.org/pub/pdb/validation_reports/jv/1jvx | HTTPS FTP |
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-Related structure data
Related structure data | 1jvyC 1mdqS S: Starting model for refinement C: citing same article (ref.) |
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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: 40951.484 Da / Num. of mol.: 1 / Mutation: D207C/A301GS/P316C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE / Plasmid: pMAL-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2058 / References: UniProt: P02928, UniProt: P0AEX9*PLUS |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#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: 2.25 Å3/Da / Density % sol: 45.26 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 6000, sodium MES, maltose, sodium azide, beta-mercaptoethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
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 RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 2, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→27.56 Å / Num. all: 12698 / Num. obs: 12533 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.5→3 Å / Mean I/σ(I) obs: 3.6 / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 24731 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MDQ Resolution: 2.5→27.56 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 946758.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: flat model / Bsol: 132.112 Å2 / ksol: 0.548925 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→27.56 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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Software | *PLUS Name: CNX / Version: 2000.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.232 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.365 / % reflection Rfree: 11.1 % / Rfactor Rwork: 0.303 |