+Open data
-Basic information
Entry | Database: PDB / ID: 1pjc | ||||||
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Title | L-ALANINE DEHYDROGENASE COMPLEXED WITH NAD | ||||||
Components | PROTEIN (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 / ISOMORPHOUS TO NATIVE / Resolution: 2 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.E. / 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 | 1pjc.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pjc.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 1pjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/1pjc ftp://data.pdbj.org/pub/pdb/validation_reports/pj/1pjc | 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 / 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-NAD / |
#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: 64.01 % |
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Crystal grow | pH: 6.7 Details: PROTEIN CRYSTALLISED FROM 0.1M MES PH 6.7 6-10% PEG 20000, SOAKED IN 10MM NAD, pH 6.70 |
-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: Feb 19, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2→18 Å / Num. obs: 188299 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.6 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS TO NATIVE / Resolution: 2→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 / Bsol: 334.3 Å2 / ksol: 0.85 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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