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Yorodumi- PDB-1goi: Crystal structure of the D140N mutant of chitinase B from Serrati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1goi | ||||||
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Title | Crystal structure of the D140N mutant of chitinase B from Serratia marcescens at 1.45 A resolution | ||||||
Components | CHITINASE B | ||||||
Keywords | HYDROLASE / CHITIN DEGRADATION / GLYCOSIDASE | ||||||
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: 1.45 Å | ||||||
Authors | Kolstad, G. / Synstad, B. / Eijsink, V.G.H. / Van Aalten, D.M.F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of the D140N Mutant of Chitinase B from Serratia Marcescens at 1.45 A Resolution. Authors: Kolstad, G. / Synstad, B. / Eijsink, V.G.H. / Van Aalten, D.M.F. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Structural Insights Into the Catalytic Mechansim of a Family 18 Exo-Chitinase 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. / Eijsink, V.G.H. / Wierenga, R.K. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY AN 10-STRANDED BARREL THESE ARE REPRESENTED BY A 11-STRANDED SHEETS 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 | 1goi.cif.gz | 444.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1goi.ent.gz | 367.1 KB | Display | PDB format |
PDBx/mmJSON format | 1goi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1goi_validation.pdf.gz | 465.4 KB | Display | wwPDB validaton report |
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Full document | 1goi_full_validation.pdf.gz | 487.3 KB | Display | |
Data in XML | 1goi_validation.xml.gz | 49 KB | Display | |
Data in CIF | 1goi_validation.cif.gz | 73.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/1goi ftp://data.pdbj.org/pub/pdb/validation_reports/go/1goi | HTTPS FTP |
-Related structure data
Related structure data | 1e15S 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
#1: Protein | Mass: 55517.027 Da / Num. of mol.: 2 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) SERRATIA MARCESCENS (bacteria) / Strain: BJL200 References: UniProt: Q54276, UniProt: P11797*PLUS, chitinase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | CHAIN A, B ENGINEERED MUTATION ASP140ASN HYDROLYSIS OF THE 1,4-BETA-LINKAGES OF N-ACETYL-D- ...CHAIN A, B ENGINEERED | |
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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: 2.09 Å3/Da / Density % sol: 41.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 100 MM HEPES, 1.25 M AMMONIUM SULPHATE, 10% GLYCEROL, pH 7.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 7 | ||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-4 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→17 Å / Num. obs: 191634 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.45→1.5 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.7 / % possible all: 99.5 |
Reflection | *PLUS Lowest resolution: 17 Å / Num. measured all: 600078 |
Reflection shell | *PLUS Lowest resolution: 1.5 Å / % possible obs: 99.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E15 Resolution: 1.45→17 Å / Num. parameters: 80913 / Num. restraintsaints: 100084 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 24 / Occupancy sum hydrogen: 7279 / Occupancy sum non hydrogen: 8885.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→17 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.164 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.1601 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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