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Yorodumi- PDB-1a04: THE STRUCTURE OF THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a04 | ||||||
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Title | THE STRUCTURE OF THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL IN THE MONOCLINIC C2 CRYSTAL FORM | ||||||
Components | NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL | ||||||
Keywords | SIGNAL TRANSDUCTION PROTEIN / RESPONSE REGULATORS / TWO-COMPONENT SYSTEMS | ||||||
Function / homology | Function and homology information DNA-binding transcription repressor activity / phosphorelay signal transduction system / nitrate assimilation / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / DNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Baikalov, I. / Schroder, I. / Kaczor-Grzeskowiak, M. / Cascio, D. / Gunsalus, R.P. / Dickerson, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: NarL dimerization? Suggestive evidence from a new crystal form Authors: Baikalov, I. / Schroder, I. / Kaczor-Grzeskowiak, M. / Cascio, D. / Gunsalus, R.P. / Dickerson, R.E. #1: Journal: Biochemistry / Year: 1996 Title: Structure of the Escherichia Coli Response Regulator NarL. Authors: Baikalov, I. / Schroder, I. / Kaczor-Grzeskowiak, M. / Grzeskowiak, K. / Gunsalus, R.P. / Dickerson, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a04.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a04.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a04_validation.pdf.gz | 417.8 KB | Display | wwPDB validaton report |
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Full document | 1a04_full_validation.pdf.gz | 420.1 KB | Display | |
Data in XML | 1a04_validation.xml.gz | 20 KB | Display | |
Data in CIF | 1a04_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a04 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a04 | HTTPS FTP |
-Related structure data
Related structure data | 1rnlS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23828.623 Da / Num. of mol.: 2 / Fragment: RESIDUES 2 - 216 OF THE WILD TYPE NARL Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Plasmid: PHXL-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10957, UniProt: P0AF28*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 51.03 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: THE PROTEIN SOLUTION CONTAINING 23.3 MG/ML OF PURIFIED NARL, 20 MM TRIS.HCL (PH=7.6), 0.5 MM MGCL2, AND 10% GLYCEROL WAS MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 0.1 M ...Details: THE PROTEIN SOLUTION CONTAINING 23.3 MG/ML OF PURIFIED NARL, 20 MM TRIS.HCL (PH=7.6), 0.5 MM MGCL2, AND 10% GLYCEROL WAS MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 0.1 M TRIS.HCL (PH=8.5), 0.2 M SODIUM ACETATE, AND 30% POLYETHYLENE GLYCOL (PEG) 4000. SITTING DROPS CONTAINING 20 ML OF MIXTURE WERE EQUILIBRATED BY VAPOR DIFFUSION AT 4 DEGREES AGAINST 20 ML OF THE RESERVOIR SOLUTION. CRYSTALS BEGAN TO APPEAR AS CLUSTERS OF PLATES AFTER 11-15 DAYS., vapor diffusion - sitting drop, temperature 277K PH range: 7.6-8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 27, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→65 Å / Num. obs: 22871 / % possible obs: 99.87 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.2→2.44 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RNL Resolution: 2.2→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Xplor file |
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