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Yorodumi- PDB-1ylv: SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ylv | ||||||
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Title | SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH LAEVULINIC ACID | ||||||
Components | PROTEIN (5-AMINOLAEVULINIC ACID DEHYDRATASE) | ||||||
Keywords | LYASE / DEHYDRATASE / ALDOLASE / TIM BARREL / TETRAPYRROLE SYNTHESIS | ||||||
Function / homology | Function and homology information Heme biosynthesis / porphobilinogen synthase / porphobilinogen synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / Neutrophil degranulation / zinc ion binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.15 Å | ||||||
Authors | Erskine, P.T. / Newbold, R. / Roper, J. / Coker, A. / Warren, M.J. / Shoolingin-Jordan, P.M. / Wood, S.P. / Cooper, J.B. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: The Schiff base complex of yeast 5-aminolaevulinic acid dehydratase with laevulinic acid. Authors: Erskine, P.T. / Newbold, R. / Roper, J. / Coker, A. / Warren, M.J. / Shoolingin-Jordan, P.M. / Wood, S.P. / Cooper, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ylv.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ylv.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ylv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ylv_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
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Full document | 1ylv_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 1ylv_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 1ylv_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/1ylv ftp://data.pdbj.org/pub/pdb/validation_reports/yl/1ylv | HTTPS FTP |
-Related structure data
Related structure data | 1aw5S 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: 37724.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: SCHIFF-BASE LINK BETWEEN LAEVULINIC ACID INHIBITOR AND LYSINE 263 Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Plasmid: PNS1 / Strain: NS1(JM109/PNS1) / References: UniProt: P05373, porphobilinogen synthase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-SHF / | ||
#4: Water | ChemComp-HOH / | ||
Nonpolymer details | INHIBITOR FORMS A SCHIFF-BASE LINK WITH LYS 263 ALTERNATIVSequence details | THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: AS FOR 1AW5 WITH 10MM LAEVULINIC ACID, pH 8.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 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: BM02 / Wavelength: 0.9799 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Oct 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→32.6 Å / Num. obs: 23348 / % possible obs: 96.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 28.95 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 6 / % possible all: 77.7 |
Reflection shell | *PLUS % possible obs: 77.7 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 1AW5 Resolution: 2.15→25 Å / Cross valid method: FREE R-FACTOR / σ(F): 3
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Displacement parameters | Biso mean: 19.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 24.8 Å / Luzzati sigma a obs: 0.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→25 Å
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Refine LS restraints |
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