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Yorodumi- PDB-1edq: CRYSTAL STRUCTURE OF CHITINASE A FROM S. MARCESCENS AT 1.55 ANGSTROMS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1edq | ||||||
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Title | CRYSTAL STRUCTURE OF CHITINASE A FROM S. MARCESCENS AT 1.55 ANGSTROMS | ||||||
Components | CHITINASE AChitinase A N-terminal domain | ||||||
Keywords | HYDROLASE / BETA-ALPHA (TIM) BARREL | ||||||
Function / homology | Function and homology information 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: 1.55 Å | ||||||
Authors | Papanikolau, Y. / Petratos, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: De novo purification scheme and crystallization conditions yield high-resolution structures of chitinase A and its complex with the inhibitor allosamidin. Authors: Papanikolau, Y. / Tavlas, G. / Vorgias, C.E. / Petratos, K. #1: Journal: Structure / Year: 1994 Title: Crystal structure of a bacterial chitinase at 2.3 Angstrom resolution Authors: Perrakis, A. / Tews, I. / Dauter, Z. / Oppenheim, A.B. / Chet, I. / Wilson, K.S. / Vorgias, C.E. #2: Journal: Biochemistry / Year: 2001 Title: HIGH RESOLUTION STRUCTURAL ANALYSES OF MUTANT CHITINASE A COMPLEXES WITH SUBSTRATES PROVIDE NEW INSIGHT INTO THE MECHANISM OF CATALYSIS Authors: PAPANIKOLAU, Y. / PRAG, G. / TAVLAS, G. / VORGIAS, C.E. / OPPENHEIM, A.B. / PETRATOS, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1edq.cif.gz | 140.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1edq.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 1edq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/1edq ftp://data.pdbj.org/pub/pdb/validation_reports/ed/1edq | HTTPS FTP |
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-Related structure data
Related structure data | 1ffqC 1ctnS 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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-Components
#1: Protein | Mass: 58639.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O83008, 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: 3.3 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.75 M Citrate-Na pH 7.2, 20% (v/v) methanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
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: 0.9116 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→10 Å / Num. all: 112857 / Num. obs: 112857 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.8 / Num. unique all: 11176 / % possible all: 100 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CTN Resolution: 1.55→10 Å / SU B: 1.328 / SU ML: 0.049 / σ(F): 0 / σ(I): 0 / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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