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Open data
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Basic information
Entry | Database: PDB / ID: 1bd0 | ||||||
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Title | ALANINE RACEMASE COMPLEXED WITH ALANINE PHOSPHONATE | ||||||
![]() | ALANINE RACEMASE | ||||||
![]() | ISOMERASE / ALANINE / PYRIDOXAL PHOSPHATE / ALANINE PHOSPHONATE | ||||||
Function / homology | ![]() alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stamper, G.F. / Morollo, A.A. / Ringe, D. | ||||||
![]() | ![]() Title: Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine. Authors: Stamper, G.F. / Morollo, A.A. / Ringe, D. / Stamper, C.G. #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: X-Ray Crystallographic Studies of the Alanine-Specific Racemase from Bacillus Stearothermophilus. Overproduction, Crystallization, and Preliminary Characterization Authors: Neidhart, D.J. / Distefano, M.D. / Tanizawa, K. / Soda, K. / Walsh, C.T. / Petsko, G.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 | ![]() | 167 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 | ![]() 1sftS 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: 43565.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.5 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM 100MM TRIS BUFFER, PH 8.5, 200MM SODIUM ACETATE, 21% PEG 4000, AND 4MM 1-AMINOETHYL PHOSPHONIC ACID. | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS / Detector: CCD / Date: Oct 30, 1996 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. obs: 97731 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 0.8 / % possible all: 93.7 |
Reflection | *PLUS Num. measured all: 516378 / Rmerge F obs: 0.078 |
Reflection shell | *PLUS % possible obs: 93.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SFT Resolution: 1.6→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.24 / Rfactor Rwork: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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