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- PDB-4era: Evidence for a Dual Role of an Active Site Histidine in alpha-Ami... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4era | ||||||
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Title | Evidence for a Dual Role of an Active Site Histidine in alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase | ||||||
![]() | 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase | ||||||
![]() | LYASE / tim-barrel / decarboxylase / Metal-binding / Co(II) | ||||||
Function / homology | ![]() secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huo, L. / Fielding, A.J. / Chen, Y. / Li, T. / Iwaki, H. / Hosler, J.P. / Chen, L. / Hasegawa, Y. / Que Jr., L. / Liu, A. | ||||||
![]() | ![]() Title: Evidence for a Dual Role of an Active Site Histidine in alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase Authors: Huo, L. / Fielding, A.J. / Chen, Y. / Li, T. / Iwaki, H. / Hosler, J.P. / Chen, L. / Hasegawa, Y. / Que, L. / Liu, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.9 KB | Display | ![]() |
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PDB format | ![]() | 110.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.1 KB | Display | ![]() |
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Full document | ![]() | 453 KB | Display | |
Data in XML | ![]() | 26.3 KB | Display | |
Data in CIF | ![]() | 35.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4epkC ![]() 4ergC ![]() 4eriC ![]() 2hbxS C: citing same article ( 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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Unit cell |
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Details | THE BIOLOGICAL UNIT IS A MONOMER. THERE ARE 2 BIOLOGICAL UNITS IN THE ASYMMETRIC UNIT (CHAIN A AND CHAIN B). |
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Components
#1: Protein | Mass: 37208.621 Da / Num. of mol.: 2 / Mutation: H228Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.75 Details: 15% PEG 5000, 0.1M Tris, 0.2M MGCL2, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.398→83.66 Å / Num. all: 26155 / Num. obs: 26385 / % possible obs: 99.13 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 40.5 |
Reflection shell | Resolution: 2.398→2.44 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.89 / Num. unique all: 1294 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HBX Resolution: 2.398→83.66 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.048 / SU ML: 0.291 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.54 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 59.574 Å2
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Refinement step | Cycle: LAST / Resolution: 2.398→83.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.398→2.46 Å / Total num. of bins used: 20
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