+Open data
-Basic information
Entry | Database: PDB / ID: 1dpp | ||||||
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Title | DIPEPTIDE BINDING PROTEIN COMPLEX WITH GLYCYL-L-LEUCINE | ||||||
Components | DIPEPTIDE BINDING PROTEIN | ||||||
Keywords | PEPTIDE BINDING PROTEIN / CHEMOTAXIS / COMPLEX (BINDING PROTEIN-PEPTIDE) COMPLEX | ||||||
Function / homology | Function and homology information dipeptide transport / dipeptide transmembrane transporter activity / heme transmembrane transport / peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chaperone-mediated protein folding / peptide binding / chemotaxis / protein transport ...dipeptide transport / dipeptide transmembrane transporter activity / heme transmembrane transport / peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chaperone-mediated protein folding / peptide binding / chemotaxis / protein transport / outer membrane-bounded periplasmic space / heme binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å | ||||||
Authors | Dunten, P. / Mowbray, S.L. | ||||||
Citation | Journal: Protein Sci. / Year: 1995 Title: Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis. Authors: Dunten, P. / Mowbray, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dpp.cif.gz | 353.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dpp.ent.gz | 303.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dpp_validation.pdf.gz | 416.4 KB | Display | wwPDB validaton report |
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Full document | 1dpp_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 1dpp_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 1dpp_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dpp ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dpp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 275 / 2: CIS PROLINE - PRO C 275 / 3: CIS PROLINE - PRO E 275 / 4: CIS PROLINE - PRO G 275 | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 57475.863 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P23847 #2: Chemical | ChemComp-GLY / #3: Chemical | ChemComp-LEU / Nonpolymer details | RESIDUES 1001 AND 1002 WITH CHAIN IDS A, C, E AND G FORM THE DIPEPTIDE SUBSTRATE BOUND TO THE ...RESIDUES 1001 AND 1002 WITH CHAIN IDS A, C, E AND G FORM THE DIPEPTIDE SUBSTRATE BOUND TO THE DIPEPTIDE-BINDING PROTEIN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.42 Å3/Da / Density % sol: 72.15 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.2 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.89 |
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Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 17, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→25 Å / Num. obs: 57483 / % possible obs: 88 % / Redundancy: 3 % / Rmerge(I) obs: 0.105 |
Reflection | *PLUS Num. measured all: 170663 / Rmerge(I) obs: 0.105 |
Reflection shell | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 3.28 Å / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Resolution: 3.2→25 Å / σ(F): 0
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Displacement parameters | Biso mean: 21.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→25 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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