+Open data
-Basic information
Entry | Database: PDB / ID: 1rd6 | ||||||
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Title | Crystal Structure of S. Marcescens Chitinase A Mutant W167A | ||||||
Components | Chitinase AChitinase A N-terminal domain | ||||||
Keywords | HYDROLASE / Chitinase A | ||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Aronson, N.N. / Halloran, B.A. / Alexyev, M.F. / Zhou, X.E. / Wang, Y. / Meehan, E.J. / Chen, L. | ||||||
Citation | Journal: Biosci.Biotechnol.Biochem. / Year: 2006 Title: Mutation of a conserved tryptophan in the chitin-binding cleft of Serratia marcescens chitinase A enhances transglycosylation. Authors: Aronson, N.N. / Halloran, B.A. / Alexeyev, M.F. / Zhou, X.E. / Wang, Y. / Meehan, E.J. / Chen, L. | ||||||
History |
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Remark 999 | The authors verified the sequence by MS and DNA sequencing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rd6.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rd6.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/1rd6 ftp://data.pdbj.org/pub/pdb/validation_reports/rd/1rd6 | HTTPS FTP |
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-Related structure data
Related structure data | 1edqS 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: 60972.434 Da / Num. of mol.: 1 / Mutation: W167A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: CHIA / Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07254, chitinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Tris,PEG 3350, (NH4)2HPO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0088 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0088 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 30623 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.413 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1edq Resolution: 2.6→19.79 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 267628.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.8689 Å2 / ksol: 0.321011 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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