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Yorodumi- PDB-1ogg: chitinase b from serratia marcescens mutant d142n in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ogg | |||||||||
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Title | chitinase b from serratia marcescens mutant d142n in complex with inhibitor allosamidin | |||||||||
Components | CHITINASE B | |||||||||
Keywords | HYDROLASE / CHITIN DEGRADATION / GLYCOSIDE HYDROLASE | |||||||||
Function / homology | Function and homology information chitinase / 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: 1.97 Å | |||||||||
Authors | Vaaje-Kolstad, G. / Houston, D.R. / Rao, F.V. / Peter, M.G. / Synstad, B. / van Aalten, D.M.F. / Eijsink, V.G.H. | |||||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2004 Title: Structure of the D142N Mutant of the Family 18 Chitinase Chib from Serratia Marcescens and its Complex with Allosamidin Authors: Vaaje-Kolstad, G. / Houston, D.R. / Rao, F.V. / Peter, M.G. / Synstad, B. / van Aalten, D.M.F. / Eijsink, V.G.H. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Structural Insights Into the Catalytic Mechanism of Family 18 Exochitinase Authors: van Aalten, D.M.F. / Komander, D. / Synstad, B. / Gaseidnes, S. / Peter, M.G. / Eijsink, V.G.H. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Structure of a Two-Domain Chitotriosidase from Serratia Marcescens at 1.9 A Resolution Authors: van Aalten, D.M.F. / Synstad, B. / Brurberg, M.B. / Hough, E. / Riise, B.W. / Eijsink, V.G.H. / Wierenga, R.K. | |||||||||
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 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 | 1ogg.cif.gz | 227.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ogg.ent.gz | 181.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ogg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1ogg ftp://data.pdbj.org/pub/pdb/validation_reports/og/1ogg | HTTPS FTP |
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-Related structure data
Related structure data | 1ogbC 1e6rS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 55517.027 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: BJL200 / Plasmid: PGEM5-Z(+) / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P11797, chitinase #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 870 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDSequence details | PROTEIN DERIVED FROM DIFFERENT S. MARCESCENS | |
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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: 2.488 Å3/Da / Density % sol: 50.62 % |
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Crystal grow | pH: 7 Details: 15 % GLYCEROL 100 MM HEPES, PH 7, 1.3 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9876 |
Detector | Date: Apr 26, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9876 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→25 Å / Num. obs: 19590 / % possible obs: 95.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E6R Resolution: 1.97→24.76 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2272779.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.735 Å2 / ksol: 0.353789 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.97→24.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.09 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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