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Yorodumi- PDB-1h7n: SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h7n | ||||||
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Title | SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH LAEVULINIC ACID AT 1.6 A RESOLUTION | ||||||
Components | 5-AMINOLAEVULINIC ACID DEHYDRATASE | ||||||
Keywords | DEHYDRATASE / LYASE / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Erskine, P.T. / Newbold, R. / Brindley, A.A. / Wood, S.P. / Shoolingin-Jordan, P.M. / Warren, M.J. / Cooper, J.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The X-Ray Structure of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed with Substrate and Three Inhibitors Authors: Erskine, P.T. / Newbold, R. / Brindley, A.A. / Wood, S.P. / Shoolingin-Jordan, P.M. / Warren, M.J. / Cooper, J.B. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-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 | 1h7n.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h7n.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/1h7n ftp://data.pdbj.org/pub/pdb/validation_reports/h7/1h7n | HTTPS FTP |
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-Related structure data
Related structure data | 1h7oC 1h7pC 1h7rC 1ylvS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37785.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SCHIFF-BASE LINK BETWEEN LAEVULINIC ACID INHIBITOR (HET GROUP A1341) AND LYSINE 263 Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05373, porphobilinogen synthase |
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#2: Chemical | ChemComp-SHF / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Sequence details | THE C-TERMINAL RESIDUES WERE 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: 2.95 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: AS FOR 1AW5 WITH 10MM LAEVULINIC ACID, pH 8.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Erskine, P.T., (1997) Protein Sci., 6, 1774. / 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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→13.1 Å / Num. obs: 59510 / % possible obs: 99.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3 / % possible all: 99.6 |
Reflection | *PLUS Highest resolution: 1.6 Å |
Reflection shell | *PLUS Highest resolution: 1.6 Å / % possible obs: 99.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YLV Resolution: 1.6→13.1 Å / Num. parameters: 12272 / Num. restraintsaints: 10981 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: THE C-TERMINAL DIPEPTIDE WAS NOT REFINED
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 4 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→13.1 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELX / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.217 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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