+Open data
-Basic information
Entry | Database: PDB / ID: 1pjb | ||||||
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Title | L-ALANINE DEHYDROGENASE | ||||||
Components | L-ALANINE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / NAD | ||||||
Function / homology | Function and homology information alanine dehydrogenase / alanine dehydrogenase activity / L-alanine catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Phormidium lapideum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / 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 | 1pjb.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pjb.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/1pjb ftp://data.pdbj.org/pub/pdb/validation_reports/pj/1pjb | 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: 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: 3.49 Å3/Da / Density % sol: 64.76 % | |||||||||||||||||||||||||
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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: Sep 29, 1996 / 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→18 Å / Num. obs: 82395 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.9 / % possible all: 91.2 |
Reflection shell | *PLUS % possible obs: 91.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / 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 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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