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- PDB-4dgu: Crystal structure of a putative cell adhesion protein (BT0320) fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dgu | ||||||
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Title | Crystal structure of a putative cell adhesion protein (BT0320) from Bacteroides thetaiotaomicron VPI-5482 at 2.37 A resolution | ||||||
![]() | putative cell adhesion protein | ||||||
![]() | CELL ADHESION / Cell adhesion protein / fimbrial related protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Immunoglobulin-like - #2670 / Immunoglobulin-like - #2680 / Fimbrillin-like 1 / Fimbrillin-like / Immunoglobulin-like / Sandwich / Mainly Beta / metal ion binding / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: A Distinct Type of Pilus from the Human Microbiome. Authors: Xu, Q. / Shoji, M. / Shibata, S. / Naito, M. / Sato, K. / Elsliger, M.A. / Grant, J.C. / Axelrod, H.L. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Deacon, A.M. / Godzik, A. / ...Authors: Xu, Q. / Shoji, M. / Shibata, S. / Naito, M. / Sato, K. / Elsliger, M.A. / Grant, J.C. / Axelrod, H.L. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Curtis, M.A. / Nakayama, K. / Wilson, I.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192 KB | Display | ![]() |
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PDB format | ![]() | 155.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.8 KB | Display | ![]() |
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Full document | ![]() | 432.9 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3liuC ![]() 3payC ![]() 3r4rC ![]() 3sy6C ![]() 3t2lC ![]() 3ufiC ![]() 3up6C ![]() 4epsC ![]() 4gpvC ![]() 4h40C ![]() 4jg5C ![]() 4jrfC ![]() 4k4kC ![]() 4q98C ![]() 4qb7C ![]() 4qdgC ![]() 4rdbC ![]() 5cagC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | CRYSTAL PACKING SUPPORTS THE ASSIGNMENT OF A DIMER OR TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE. |
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Components
#1: Protein | Mass: 26533.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: VPI-5482 / Gene: BT_0320 / Plasmid: SpeedET / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.17 Details: 0.2M zinc acetate, 10.0% polyethylene glycol 8000, 0.1M MES pH 6.17, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011 Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.37→36.91 Å / Num. obs: 23861 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 58.262 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.06 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ZINC FROM CRYSTALLIZATION CONDITION, CHLORIDE (CL) FROM THE EXPRESSION OR PURIFICATION BUFFERS ARE MODELED INTO THE STRUCTURE. THE MODELING OF ZINC IS SUPPORTED BY ANOMALOUS DIFFERENCE MAPS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
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Displacement parameters | Biso max: 150.72 Å2 / Biso mean: 59.4027 Å2 / Biso min: 26.96 Å2
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Refine analyze | Luzzati coordinate error obs: 0.341 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→36.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.37→2.48 Å / Total num. of bins used: 12
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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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