+Open data
-Basic information
Entry | Database: PDB / ID: 1l6g | ||||||
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Title | Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine | ||||||
Components | alanine racemase | ||||||
Keywords | ISOMERASE / alanine racemase / reaction mechanism / N-(5'-phosphopyridoxyl)-alanine | ||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Watanabe, A. / Yoshimura, T. / Mikami, B. / Hayashi, H. / Kagamiyama, H. / Esaki, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 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: Journal: Biochemistry / Year: 1997 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: Journal: Biochemistry / Year: 1998 Title: Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine Authors: Stamper, G.F. / Morollo, A.A. / Ringe, D. #3: Journal: Biochemistry / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l6g.cif.gz | 166.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l6g.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 1l6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/1l6g ftp://data.pdbj.org/pub/pdb/validation_reports/l6/1l6g | HTTPS FTP |
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-Related structure data
Related structure data | 1l6fSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Geobacillus stearothermophilus (bacteria) Plasmid: pAR310 / Production host: Escherichia coli (E. coli) / References: UniProt: P10724, alanine racemase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.27 % | ||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 16, 1998 / Details: carbon monochrometer |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→38.76 Å / Num. all: 50473 / Num. obs: 50473 / % possible obs: 86.87 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 7 Å2 / Rsym value: 0.077 / Net I/σ(I): 6.67 |
Reflection shell | Resolution: 1.939→2.009 Å / Redundancy: 1.81 % / Mean I/σ(I) obs: 1.64 / Num. unique all: 5583 / Rsym value: 0.496 / % possible all: 76.1 |
Reflection | *PLUS % possible obs: 86.9 % / Num. measured all: 201757 / Rmerge(I) obs: 0.077 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1L6F Resolution: 2→7.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 591826.07 / 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: 93.3228 Å2 / ksol: 0.407277 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→7.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.14 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.254 |