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Open data
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Basic information
Entry | Database: PDB / ID: 1l6f | ||||||
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Title | Alanine racemase bound with N-(5'-phosphopyridoxyl)-L-alanine | ||||||
![]() | alanine racemase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Watanabe, A. / Yoshimura, T. / Mikami, B. / Hayashi, H. / Kagamiyama, H. / Esaki, N. | ||||||
![]() | ![]() Title: Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine. Authors: Watanabe, A. / Yoshimura, T. / Mikami, B. / Hayashi, H. / Kagamiyama, H. / Esaki, N. #1: ![]() Title: Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution Authors: Shaw, J.P. / Petsko, G.A. / Ringe, D. #2: ![]() Title: Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine Authors: Stamper, G.F. / Morollo, A.A. / Ringe, D. #3: ![]() Title: Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase Authors: Morollo, A.A. / Petsko, G.A. / Ringe, 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 | ![]() | 168.3 KB | Display | ![]() |
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PDB format | ![]() | 133.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1l6gC ![]() 1sftS 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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Components
#1: Protein | ![]() Mass: 43695.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Plasmid: pAR310 / Production host: ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.55 % | ||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, sodium acetate, Tris-buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 15, 1998 / Details: carbon monochrometer |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.93→43.1 Å / Num. all: 52427 / Num. obs: 52427 / % possible obs: 88.39 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 6.1 Å2 / Rsym value: 0.088 / Net I/σ(I): 1.48 |
Reflection shell | Resolution: 1.929→1.998 Å / Redundancy: 1.82 % / Mean I/σ(I) obs: 1.48 / Num. unique all: 2412 / Rsym value: 0.476 / % possible all: 73.2 |
Reflection | *PLUS % possible obs: 88.4 % / Num. measured all: 199015 / Rmerge(I) obs: 0.088 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1SFT Resolution: 2→7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 493425.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 116.24 Å2 / ksol: 0.486264 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 7 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.88 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.26 |