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- PDB-5fq7: Crystal structure of the SusCD complex BT2261-2264 from Bacteroid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fq7 | ||||||
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Title | Crystal structure of the SusCD complex BT2261-2264 from Bacteroides thetaiotaomicron | ||||||
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![]() | MEMBRANE PROTEIN / SUGAR BINDING PROTEIN / OUTER MEMBRANE NUTRIENT IMPORTER SUSCD COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Glenwright, A.J. / Pothula, K.R. / Chorev, D.S. / Basle, A. / Robinson, C.V. / Kleinekathoefer, U. / Bolam, D.N. / van den Berg, B. | ||||||
![]() | ![]() Title: Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Authors: Glenwright, A.J. / Pothula, K.R. / Bhamidimarri, S.P. / Chorev, D.S. / Basle, A. / Firbank, S.J. / Zheng, H. / Robinson, C.V. / Winterhalter, M. / Kleinekathofer, U. / Bolam, D.N. / van den Berg, B. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 23-STRANDED BARREL THIS IS REPRESENTED BY A 24-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 519.8 KB | Display | ![]() |
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Full document | ![]() | 583.7 KB | Display | |
Data in XML | ![]() | 113.4 KB | Display | |
Data in CIF | ![]() | 155.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fq3SC ![]() 5fq4SC ![]() 5fq6C ![]() 5fq8C ![]() 5lx8C ![]() 5t3rC ![]() 5t4yC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 4 types, 8 molecules ACBDEFGH
#1: Protein | Mass: 53145.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) ![]() #2: Protein | Mass: 108954.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TONB DEPENDENT TRANSPORTER / Source: (natural) ![]() #3: Protein | Mass: 16428.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) ![]() #4: Protein | Mass: 23399.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) ![]() |
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-Protein/peptide , 1 types, 2 molecules IP
#5: Protein/peptide | Mass: 588.533 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 2 types, 8 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/NA.gif)
#6: Chemical | #7: Chemical | ChemComp-NA / |
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-Details
Sequence details | IDENTITY OF PEPTIDE IS UNKNOWN. FITTED SEQUENCE PROVIDES A REASONABLE FIT TO THE DENSITY. PROBABLY ...IDENTITY OF PEPTIDE IS UNKNOWN. FITTED SEQUENCE PROVIDES A REASONABLE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % / Description: ORTHORHOMBIC CRYSTAL FORM |
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Crystal grow | Details: 0.2 M MAGNESIUM FORMATE DIHYDRATE 0.05 M TRIS PH 8 18-22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Jan 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→49.45 Å / Num. obs: 76187 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3.4→3.47 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 5FQ4, 5FQ3 Resolution: 3.4→48.432 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 24.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→48.432 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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