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Yorodumi- PDB-4jg5: Crystal structure of a putative cell adhesion protein (BDI_3519) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jg5 | ||||||
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Title | Crystal structure of a putative cell adhesion protein (BDI_3519) from Parabacteroides distasonis ATCC 8503 at 2.34 A resolution (PSI Community Target, Nakayama) | ||||||
Components | Putative cell adhesion protein | ||||||
Keywords | CELL ADHESION / Major fimbrial subunit protein (FimA) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Parabacteroides distasonis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.34 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Cell / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jg5.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jg5.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 4jg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jg5_validation.pdf.gz | 421.7 KB | Display | wwPDB validaton report |
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Full document | 4jg5_full_validation.pdf.gz | 423.5 KB | Display | |
Data in XML | 4jg5_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 4jg5_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/4jg5 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/4jg5 | HTTPS FTP |
-Related structure data
Related structure data | 3liuC 3payC 3r4rC 3sy6C 3t2lC 3ufiC 3up6C 4dguC 4epsC 4gpvC 4h40C 4jrfC 4k4kC 4q98C 4qb7C 4qdgC 4rdbC 5cagC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39221.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_3519 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LHQ6 |
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#2: Water | ChemComp-HOH / |
Sequence details | SEQUENCE THE CONSTRUCT (22-375) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...SEQUENCE THE CONSTRUCT (22-375) WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.29 Details: 28.6% polyethylene glycol 4000, 0.2M sodium acetate, 0.1M TRIS pH 8.29, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97853 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.34→48.997 Å / Num. obs: 15739 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.24 % / Biso Wilson estimate: 48.787 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.34→48.997 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9049 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
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Displacement parameters | Biso max: 144.67 Å2 / Biso mean: 48.8497 Å2 / Biso min: 20.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.299 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→48.997 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.34→2.5 Å / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: 12.3156 Å / Origin y: 56.4124 Å / Origin z: 6.5862 Å
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Refinement TLS group | Selection details: {A|29 - 371} |