+Open data
-Basic information
Entry | Database: PDB / ID: 1bd0 | ||||||
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Title | ALANINE RACEMASE COMPLEXED WITH ALANINE PHOSPHONATE | ||||||
Components | ALANINE RACEMASE | ||||||
Keywords | ISOMERASE / ALANINE / PYRIDOXAL PHOSPHATE / ALANINE PHOSPHONATE | ||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / cytosol Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Stamper, G.F. / Morollo, A.A. / Ringe, D. | ||||||
Citation | 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. / Stamper, C.G. #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: J.Biol.Chem. / Year: 1987 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bd0.cif.gz | 167 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bd0.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bd0_validation.pdf.gz | 511.4 KB | Display | wwPDB validaton report |
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Full document | 1bd0_full_validation.pdf.gz | 524.7 KB | Display | |
Data in XML | 1bd0_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1bd0_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/1bd0 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/1bd0 | HTTPS FTP |
-Related structure data
Related structure data | 1sftS S: Starting model for refinement |
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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: 43565.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / Plasmid: PMDALR3 / Strain: XL-1 BLUE / 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: 2.12 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: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.24 / Rfactor Rwork: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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