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Yorodumi- PDB-1e6r: Chitinase B from Serratia marcescens wildtype in complex with inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e6r | |||||||||
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Title | Chitinase B from Serratia marcescens wildtype in complex with inhibitor allosamidin | |||||||||
Components | CHITINASE B | |||||||||
Keywords | HYDROLASE / CHITIN DEGRADATION / INHIBITOR ALLOSAMIDIN | |||||||||
Function / homology | Function and homology information chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | SERRATIA MARCESCENS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Komander, D. / Synstad, B. / Eijsink, V.G.H. / Van Aalten, D.M.F. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Structural Insights Into the Catalytic Mechanism of a Family 18 Exo-Chitinase Authors: Van Aalten, D.M.F. / Komander, D. / Synstad, B. / Gseidnes, S. / Peter, M.G. / Eijsink, V.G.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e6r.cif.gz | 209 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e6r.ent.gz | 167.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e6r_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1e6r_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1e6r_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 1e6r_validation.cif.gz | 57 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/1e6r ftp://data.pdbj.org/pub/pdb/validation_reports/e6/1e6r | HTTPS FTP |
-Related structure data
Related structure data | 1e6nC 1e6pC 1e6zC 1e15S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1),Details | BIOLOGICAL_UNIT: DIMERIC IN CRYSTAL, ACTIVE AS A MONOMER | |
-Components
#1: Protein | Mass: 55518.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q54276 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Sequence details | SOME RESIDUES MUTATED TO ACCOUNT FOR MISSING DENSITY | |
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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: 2.5 Å3/Da / Density % sol: 50.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 2.0M AMMONIUM SULFATE, 20% GLYCEROL, HEPES PH7.0, pH 7.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, hanging dropDetails: Van Aalten, D.M.F., (2000) Proc. Natl. Acad. Sci. U.S.A., 97, 5842. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9073 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 12, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9073 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 139537 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 37616 / Num. measured all: 139537 |
Reflection shell | *PLUS % possible obs: 99.9 % / Num. unique obs: 3679 / Num. measured obs: 13502 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E15 Resolution: 2.5→24.9 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2018903.18 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.3871 Å2 / ksol: 0.367362 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→24.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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