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Yorodumi- PDB-1w31: YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 5-HYDROXYLAEVULINIC ACID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w31 | ||||||
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Title | YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 5-HYDROXYLAEVULINIC ACID COMPLEX | ||||||
Components | DELTA-AMINOLEVULINIC ACID DEHYDRATASE | ||||||
Keywords | LYASE / DEHYDRATASE / ALDOLASE / TIM BARREL / TETRAPYRROLE SYNTHESIS / HEME BIOSYNTHESIS / ZINC | ||||||
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: 1.9 Å | ||||||
Authors | Erskine, P.T. / Coates, L. / Newbold, R. / Brindley, A.A. / Stauffer, F. / Beaven, G.D.E. / Gill, R. / Wood, S.P. / Warren, M.J. / Cooper, J.B. ...Erskine, P.T. / Coates, L. / Newbold, R. / Brindley, A.A. / Stauffer, F. / Beaven, G.D.E. / Gill, R. / Wood, S.P. / Warren, M.J. / Cooper, J.B. / Shoolingin-Jordan, P.M. / Neier, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed with the Inhibitor 5-Hydroxylaevulinic Acid Authors: Erskine, P.T. / Coates, L. / Newbold, R. / Brindley, A.A. / Stauffer, F. / Beaven, G.D.E. / Gill, R. / Coker, A. / Wood, S.P. / Warren, M.J. / Shoolingin-Jordan, P.M. / Neier, R. / 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 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-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 | 1w31.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w31.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/1w31 ftp://data.pdbj.org/pub/pdb/validation_reports/w3/1w31 | HTTPS FTP |
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-Related structure data
Related structure data | 1ylvS 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: 37785.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH 5-HYDROXYLAEVULINIC ACID Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: NS1(JM109/PNS1) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05373, porphobilinogen synthase |
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#2: Chemical | ChemComp-SHO / |
#3: Chemical | ChemComp-ZN / |
#4: 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: 2.91 Å3/Da / Density % sol: 57 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: ENZYME CONCENTRATION 1 MG/ML, PH 7.0 - 8.5, BUFFER 0.2 M TRIS-HCL, PRECIPITANT PEG 6000 (<10%), 70 MICROMOLAR ZINC SULPHATE, 6 MM BETA-MERCAPTOETHANOL, HANGING DROPS AS FOR PDB ENTRY 1AW5 WITH 10 MM 5-HYDROXYLAEVULINIC ACID IN DROP. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.911662 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 16, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.911662 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49 Å / Num. obs: 1067852 / % possible obs: 100 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 10 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YLV Resolution: 1.9→44.28 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.9→44.28 Å
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Refinement | *PLUS Rfactor obs: 0.1895 / Rfactor Rfree: 0.2493 / Rfactor Rwork: 0.1895 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |