+Open data
-Basic information
Entry | Database: PDB / ID: 1say | |||||||||
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Title | L-ALANINE DEHYDROGENASE COMPLEXED WITH PYRUVATE | |||||||||
Components | L-ALANINE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / NAD | |||||||||
Function / homology | Function and homology information alanine dehydrogenase / alanine dehydrogenase activity / L-alanine catabolic process / nucleotide binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Phormidium lapideum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH NATIVE ENZYME / Resolution: 2.1 Å | |||||||||
Authors | Baker, P.J. / Sawa, Y. / Shibata, H. / Sedelnikova, S.E. / Rice, D.W. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase. Authors: Baker, P.J. / Sawa, Y. / Shibata, H. / Sedelnikova, S.E. / Rice, D.W. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization of the Alanine Dehydrogenase from Phormidium Lapideum Authors: Sedelnikova, S. / Rice, D.W. / Shibata, H. / Sawa, Y. / Baker, P.J. #2: Journal: J.Biochem.(Tokyo) / Year: 1994 Title: Purification and Characterization of Alanine Dehydrogenase from a Cyanobacterium, Phormidium Lapideum Authors: Sawa, Y. / Tani, M. / Murata, K. / Shibata, H. / Ochiai, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1say.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1say.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 1say.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/1say ftp://data.pdbj.org/pub/pdb/validation_reports/sa/1say | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38592.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phormidium lapideum (bacteria) / Description: MATSUE HOT SPRINGS / Gene: ALADH / Plasmid: PNAD1 / Gene (production host): ALADH / Production host: Escherichia coli (E. coli) / Strain (production host): MV1184 / References: UniProt: O52942, alanine dehydrogenase |
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#2: Chemical | ChemComp-PYR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 63.99 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.7 / Details: pH 6.7 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 63279 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.5 / % possible all: 99.1 |
Reflection shell | *PLUS % possible obs: 99.1 % |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH NATIVE ENZYME Resolution: 2.1→30 Å / Isotropic thermal model: TNT / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS AND KRETSINGER | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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