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- PDB-1ibw: STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE BOUND ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ibw | ||||||||||||
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Title | STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE BOUND WITH HISTIDINE METHYL ESTER AT 25 C | ||||||||||||
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![]() | LYASE / SUBSTRATE-INDUCED ACTIVATION / ACTIVE FORM / SITE-DIRECTED MUTANT / PYRUVOYL / CARBOXY-LYASE | ||||||||||||
Function / homology | ![]() histidine decarboxylase / histidine decarboxylase activity / L-histidine metabolic process / amino acid metabolic process Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Worley, S. / Schelp, E. / Monzingo, A.F. / Ernst, S. / Robertus, J.D. | ||||||||||||
![]() | ![]() Title: Structure and cooperativity of a T-state mutant of histidine decarboxylase from Lactobacillus 30a. Authors: Worley, S. / Schelp, E. / Monzingo, A.F. / Ernst, S. / Robertus, J.D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.4 KB | Display | ![]() |
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PDB format | ![]() | 150.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.9 KB | Display | ![]() |
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Full document | ![]() | 508.2 KB | Display | |
Data in XML | ![]() | 36.3 KB | Display | |
Data in CIF | ![]() | 48 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ibtC ![]() 1ibuC ![]() 1ibvC ![]() 1pyaS 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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Details | The biological assembly is a hexamer generated by applying a crystallographic two-fold to the trimer in the asymmetric unit: -x, y, -z + 1/2 |
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Components
#1: Protein | Mass: 8848.862 Da / Num. of mol.: 3 / Fragment: BETA CHAIN (RESIDUES 1-81) / Mutation: D53N, D54N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 25285.375 Da / Num. of mol.: 3 / Fragment: ALPHA CHAIN (RESIDUES 82-310) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.14 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 400, PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 21, 2000 |
Radiation | Monochromator: DOUBLE FOCUSSING MIRRORS (NI & PT) + NI FILTER Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. all: 15945 / Num. obs: 15945 / % possible obs: 80.7 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 66.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.454 / % possible all: 84.8 |
Reflection | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 20 Å / Redundancy: 1.8 % |
Reflection shell | *PLUS Mean I/σ(I) obs: 2.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PYA Resolution: 3.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |