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- PDB-5hnr: The X-ray structure of octameric human native 5-aminolaevulinic a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hnr | |||||||||
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Title | The X-ray structure of octameric human native 5-aminolaevulinic acid dehydratase. | |||||||||
![]() | Delta-aminolevulinic acid dehydratase | |||||||||
![]() | LYASE / Tetrapyrrole biosynthesis enzyme / TIM barrel / substrate complex. | |||||||||
Function / homology | ![]() proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / negative regulation of proteasomal protein catabolic process / response to aluminum ion ...proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / negative regulation of proteasomal protein catabolic process / response to aluminum ion / cellular response to lead ion / response to mercury ion / response to selenium ion / protoporphyrinogen IX biosynthetic process / response to fatty acid / response to cobalt ion / response to methylmercury / response to arsenic-containing substance / response to iron ion / response to herbicide / Heme biosynthesis / heme biosynthetic process / response to ionizing radiation / response to zinc ion / response to vitamin E / response to amino acid / catalytic activity / cellular response to interleukin-4 / response to cadmium ion / response to glucocorticoid / response to activity / protein homooligomerization / secretory granule lumen / response to ethanol / response to oxidative stress / ficolin-1-rich granule lumen / response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / Neutrophil degranulation / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mills-Davies, N.L. / Thompson, D. / Shoolingin-Jordan, P.M. / Erskine, P.T. / Cooper, J.B. | |||||||||
![]() | ![]() Title: Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis. Authors: Mills-Davies, N. / Butler, D. / Norton, E. / Thompson, D. / Sarwar, M. / Guo, J. / Gill, R. / Azim, N. / Coker, A. / Wood, S.P. / Erskine, P.T. / Coates, L. / Cooper, J.B. / Rashid, N. / ...Authors: Mills-Davies, N. / Butler, D. / Norton, E. / Thompson, D. / Sarwar, M. / Guo, J. / Gill, R. / Azim, N. / Coker, A. / Wood, S.P. / Erskine, P.T. / Coates, L. / Cooper, J.B. / Rashid, N. / Akhtar, M. / Shoolingin-Jordan, P.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.2 KB | Display | ![]() |
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PDB format | ![]() | 106 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.2 KB | Display | ![]() |
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Full document | ![]() | 469.9 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hmsC ![]() 5lzlC ![]() 5mhbC ![]() 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
#1: Protein | Mass: 36338.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-ZN / | #3: Chemical | #4: Chemical | ChemComp-DAV / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 10 mg/ml protein concentration in 10 milliM Tris pH 7.4, 10 milliM diothiothreitol and 100 microM zinc chloride. 5 microlitres of this were mixed with an equal volume of 0.1 M MES pH range 6. ...Details: 10 mg/ml protein concentration in 10 milliM Tris pH 7.4, 10 milliM diothiothreitol and 100 microM zinc chloride. 5 microlitres of this were mixed with an equal volume of 0.1 M MES pH range 6.2 - 6.5, 1.0 - 1.6 M ammonium sulphate and 0 - 10 % dioxane. PH range: 6.2 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→54.2 Å / Num. all: 18652 / Num. obs: 18652 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.8→3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.9 / % possible all: 76.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1aw5 Resolution: 2.83→44.38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.612 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.13 Å2
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Refinement step | Cycle: 1 / Resolution: 2.83→44.38 Å
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