+Open data
-Basic information
Entry | Database: PDB / ID: 1ogb | ||||||
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Title | Chitinase b from Serratia marcescens mutant D142N | ||||||
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 / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | SERRATIA MARCESCENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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 "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP 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 | 1ogb.cif.gz | 238.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ogb.ent.gz | 191.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ogb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1ogb ftp://data.pdbj.org/pub/pdb/validation_reports/og/1ogb | HTTPS FTP |
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-Related structure data
Related structure data | 1oggC 1goiS 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
#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: Q54276, UniProt: P11797*PLUS, chitinase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | PROTEIN DERIVED FROM 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: 2.47 Å3/Da / Density % sol: 48 % |
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Crystal grow | pH: 7 Details: 100 MM HEPES PH 7.0, 15% GLYCEROL 1.3 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Feb 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→15 Å / Num. obs: 90699 / % possible obs: 96.7 % / Redundancy: 3 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 8.1 / % possible all: 82.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GOI Resolution: 1.85→14.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2485525.44 / 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: 55.1837 Å2 / ksol: 0.371813 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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