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- PDB-5cag: Crystal structure of a putative adhesin (BACOVA_02677) from Bacte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cag | ||||||
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Title | Crystal structure of a putative adhesin (BACOVA_02677) from Bacteroides ovatus ATCC 8483 at 3.00 A resolution (PSI Community Target, Nakayama) | ||||||
![]() | Uncharacterized protein | ||||||
![]() | CELL ADHESION / adhesin / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Protein of unknown function DUF5119 / Domain of unknown function (DUF5119) / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Putative fimbrium anchoring subunit Fim4B![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) / Nakayama, K. | ||||||
![]() | ![]() 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 | ![]() | 127 KB | Display | ![]() |
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PDB format | ![]() | 104.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.9 KB | Display | ![]() |
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Full document | ![]() | 441.5 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3liuC ![]() 3payC ![]() 3r4rC ![]() 3sy6C ![]() 3t2lC ![]() 3ufiC ![]() 3up6C ![]() 4dguC ![]() 4epsC ![]() 4gpvC ![]() 4h40C ![]() 4jg5C ![]() 4jrfC ![]() 4k4kC ![]() 4q98C ![]() 4qb7C ![]() 4qdgC ![]() 4rdbC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35280.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 0.2000M lithium sulfate, 2.0000M ammonium sulfate, 0.1M CAPS pH 10.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2014 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: 3→49.195 Å / Num. obs: 13098 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.491 % / Biso Wilson estimate: 81.271 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.098 / Net I/σ(I): 18.18 / Num. measured all: 125002 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 5. THE SEQUENCE IS NUMBERED ACCORDING PATRIC DB ENTRY VBIBacOva42630_2252 WHICH CONTAINS ADDITIONAL N-TERM SIGNAL SEQUENCE (NOT PRESENT IN UNIPROT ENTRY VBIBacOva42630_2252).
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Displacement parameters | Biso max: 225.89 Å2 / Biso mean: 107.9401 Å2 / Biso min: 59.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.564 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.195 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.24 Å / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: 25.9473 Å / Origin y: 60.0926 Å / Origin z: 117.583 Å
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Refinement TLS group | Selection details: {A|0 - 306} |