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- PDB-1gjp: SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE W... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gjp | ||||||
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Title | SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH 4-OXOSEBACIC ACID | ||||||
![]() | 5-AMINOLAEVULINIC ACID DEHYDRATASE | ||||||
![]() | DEHYDRATASE / LYASE / ALDOLASE / TIM BARREL / TETRAPYRROLE SYNTHESIS | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Erskine, P.T. / Coates, L. / Newbold, R. / Brindley, A.A. / Wood, S.P. / Warren, M.J. / Cooper, J.B. / Shoolingin-Jordan, P.M. / Neier, R. | ||||||
![]() | ![]() Title: The X-Ray Structure of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed with Two Diacid Inhibitors Authors: Erskine, P.T. / Coates, L. / Newbold, R. / Brindley, A.A. / Stauffer, F. / Wood, S.P. / Warren, M.J. / Cooper, J.B. / Shoolingin-Jordan, P.M. / Neier, R. | ||||||
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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.5 KB | Display | ![]() |
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PDB format | ![]() | 69.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1eb3C ![]() 1aw5S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 37541.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SCHIFF-BASE LINK BETWEEN 4-OXOSEBACIC ACID SUBSTRATE (HET GROUP A363) AND LYSINE 263 Source: (gene. exp.) ![]() ![]() Strain: NS1(JM109/PNS1) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-4OX / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Sequence details | THE LAST TWO RESIDUES AT THE C-TERMINAL WERE NOT SEEN IN THE DENSITY MAPS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: AS FOR 1AW5 WITH 5MM 4-OXOSEBACIC ACID IN DROP, 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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30.4 Å / Num. obs: 39906 / % possible obs: 94.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.5 / % possible all: 87.7 |
Reflection shell | *PLUS % possible obs: 87.7 % / Mean I/σ(I) obs: 1.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AW5 Resolution: 1.8→30.4 Å / Num. parameters: 12815 / Num. restraintsaints: 11222 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30.4 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97/2 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.265 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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