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Yorodumi- PDB-1f6p: CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f6p | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM III | ||||||
Components | N-ACETYL NEURAMINATE LYASE | ||||||
Keywords | LYASE / BETA BARREL | ||||||
Function / homology | Function and homology information N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | ||||||
Authors | Barbosa, J.A.R.G. / Smith, B.J. / DeGori, R. / Lawrence, M.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Active site modulation in the N-acetylneuraminate lyase sub-family as revealed by the structure of the inhibitor-complexed Haemophilus influenzae enzyme. Authors: Barbosa, J.A.R.G. / Smith, B.J. / DeGori, R. / Ooi, H.C. / Marcuccio, S.M. / Campi, E.M. / Jackson, W.R. / Brossmer, R. / Sommer, M. / Lawrence, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f6p.cif.gz | 239.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f6p.ent.gz | 194.9 KB | Display | PDB format |
PDBx/mmJSON format | 1f6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/1f6p ftp://data.pdbj.org/pub/pdb/validation_reports/f6/1f6p | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer from chains A, B, C, and D. |
-Components
#1: Protein | Mass: 32561.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: PKKTAC / Production host: Escherichia coli (E. coli) / References: UniProt: P44539, N-acetylneuraminate lyase #2: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47.57 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, sodium acetate, ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 29, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. all: 58826 / Num. obs: 58235 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.39 / Num. unique all: 2872 / % possible all: 97.6 |
Reflection | *PLUS Num. measured all: 264983 |
Reflection shell | *PLUS % possible obs: 97.6 % / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
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Refinement | Resolution: 2.25→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.188 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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