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Yorodumi- PDB-2bh0: Crystal structure of a SeMet derivative of EXPA from Bacillus sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bh0 | ||||||
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Title | Crystal structure of a SeMet derivative of EXPA from Bacillus subtilis at 2.5 angstrom | ||||||
Components | YOAJ | ||||||
Keywords | CELL ADHESION / EXPANSIN RELATED PROTEIN / BACILLUS SUBTILIS / EXPANSINS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Petrella, S. / Herman, R. / Sauvage, E. / Filee, P. / Joris, B. / Charlier, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Crystal Structure and Activity of Bacillus Subtilis Yoaj (Exlx1), a Bacterial Expansin that Promotes Root Colonization. Authors: Kerff, F. / Amoroso, A. / Herman, R. / Sauvage, E. / Petrella, S. / Fileee, P. / Charlier, P. / Joris, B. / Tabuchi, A. / Nikolaidis, N. / Cosgrove, D.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bh0.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bh0.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/2bh0 ftp://data.pdbj.org/pub/pdb/validation_reports/bh/2bh0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23471.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS SUBTILIS (bacteria) / Strain: 168 / References: UniProt: O34918 |
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#2: Water | ChemComp-HOH / |
Compound details | EXPANSINS ARE PLANT CELL WALL PROTEINS FIRST DISCOVERED IN STUDIES OF PLANT CELL ENLARGEMENT. THEY ...EXPANSINS ARE PLANT CELL WALL PROTEINS FIRST DISCOVERED |
Sequence details | THE SIGNAL PEPTIDE OF THE PROTEIN USED FOR THE CRYSTALLIS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.19 Å3/Da / Density % sol: 76 % |
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Crystal grow | Details: 4M NAFORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 6, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25.46 Å / Num. obs: 17348 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 21.8 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 21.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 5.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→25.46 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2987475.25 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.875 Å2 / ksol: 0.418993 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→25.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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