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Yorodumi- PDB-2bem: Crystal structure of the Serratia marcescens chitin-binding prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bem | ||||||
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Title | Crystal structure of the Serratia marcescens chitin-binding protein CBP21 | ||||||
Components | CBP21 | ||||||
Keywords | CHITIN-BINDING PROTEIN / CHITIN DEGRADATION / CHITIN-BINDING / FNIII-LIKE FOLD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SERRATIA MARCESCENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Vaaje-Kolstad, G. / Houston, D.R. / Eijsink, V.G.H. / van Aalten, D.M.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal Structure and Binding Properties of the Serratia Marcescens Chitin-Binding Protein Cbp21 Authors: Vaaje-Kolstad, G. / Houston, D.R. / Eijsink, V.G.H. / Van Aalten, D.M.F. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bem.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bem.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bem_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 2bem_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 2bem_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 2bem_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2bem ftp://data.pdbj.org/pub/pdb/validation_reports/be/2bem | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 18812.832 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: BJL200 / Plasmid: PRSETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O83009 #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 40.2 % |
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Crystal grow | pH: 7.5 / Details: 1.26 AMMONIUM SULPHATE 0.1 M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 0.89 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 21, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→25 Å / Num. obs: 69645 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 42.4 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 6.9 / % possible all: 83.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→24.21 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1601050.11 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.1678 Å2 / ksol: 0.353416 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→24.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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