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- PDB-1b4k: High resolution crystal structure of a MG2-dependent 5-aminolevul... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1b4k | ||||||
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Title | High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase | ||||||
![]() | PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE) | ||||||
![]() | LYASE / HEME BIOSYNTHESIS / MAGNESIUM / LEVULINIC ACID | ||||||
Function / homology | ![]() porphobilinogen synthase / porphobilinogen synthase activity / porphyrin-containing compound biosynthetic process / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frankenberg, N. / Jahn, D. / Heinz, D.W. | ||||||
![]() | ![]() Title: High resolution crystal structure of a Mg2+-dependent porphobilinogen synthase. Authors: Frankenberg, N. / Erskine, P.T. / Cooper, J.B. / Shoolingin-Jordan, P.M. / Jahn, D. / Heinz, D.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.4 KB | Display | ![]() |
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PDB format | ![]() | 116.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.3 KB | Display | ![]() |
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Full document | ![]() | 481.1 KB | Display | |
Data in XML | ![]() | 32.4 KB | Display | |
Data in CIF | ![]() | 48.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1aw5S S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.812422, 0.582386, -0.02822), Vector: |
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Components
#1: Protein | Mass: 37077.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SCHIFF BASE LINK BETWEEN ATOM NZ OF LYS260 AND ATOM C4 OF LEVULINIC ACID Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | CARBONYL OXYGEN OF LEVULINIC ACID MISSING CARBONYL OXYGEN OF LEVULINIC ACID MISSING BECAUSE OF SCHIFF | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging dropDetails: drop contained equal volume of protein and reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→51.3 Å / Num. obs: 81840 / % possible obs: 98.2 % / Redundancy: 8.8 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.054 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.269 / % possible all: 94.1 |
Reflection | *PLUS Num. measured all: 719706 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 94.1 % / Rmerge(I) obs: 0.269 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AW5 Resolution: 1.67→51.3 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.18
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Displacement parameters | Biso mean: 19.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→51.3 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 81840 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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