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Yorodumi- PDB-1zg1: NarL complexed to nirB promoter non-palindromic tail-to-tail DNA site -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zg1 | ||||||
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Title | NarL complexed to nirB promoter non-palindromic tail-to-tail DNA site | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / protein-DNA complex / helix-turn-helix / two-component response regulator / dna bending / TRANSCRIPTION-DNA COMPLEX | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Maris, A.E. / Kaczor-Grzeskowiak, M. / Ma, Z. / Kopka, M.L. / Gunsalus, R.P. / Dickerson, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Primary and Secondary Modes of DNA Recognition by the NarL Two-Component Response Regulator. Authors: Maris, A.E. / Kaczor-Grzeskowiak, M. / Ma, Z. / Kopka, M.L. / Gunsalus, R.P. / Dickerson, R.E. #1: Journal: Nat.Struct.Biol. / Year: 2002 Title: Dimerization allows DNA target site recognition by the NarL response regulator Authors: Maris, A.E. / Sawaya, M.R. / Kaczor-Grzeskowiak, M. / Jarvis, M.R. / Bearson, S.M.D. / Kopka, M.L. / Schroeder, I. / Gunsalus, R.P. / Dickerson, R.E. #2: Journal: Biochemistry / Year: 1996 Title: Structure of the Escherichia coli response regulator NarL Authors: Baikalov, I. / Schroeder, 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 | 1zg1.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zg1.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/1zg1 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/1zg1 | HTTPS FTP |
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-Related structure data
Related structure data | 1zg5C 1je8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit is a dimer bound to DNA. There are two biological units in the asymmetric unit (chains A, B, C & D and chains E, F, G & H) |
-Components
#1: DNA chain | Mass: 6124.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid phase synthesis #2: DNA chain | Mass: 6142.993 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid phase synthesis #3: Protein | Mass: 9827.909 Da / Num. of mol.: 4 / Fragment: DNA binding domain (residues 147-216) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narL, frdR / Plasmid: pMJ05 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0AF28 #4: Chemical | ChemComp-SO4 / #5: 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: 2.7 Å3/Da / Density % sol: 54.4 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium sulfate, pH 7.5, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→25 Å / Num. all: 32539 / Num. obs: 32539 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.067 / Χ2: 0.989 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.25→2.3 Å / % possible obs: 98.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.9 / Num. measured obs: 1942 / Num. unique all: 1942 / Rsym value: 0.469 / Χ2: 1.047 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JE8 Resolution: 2.3→9 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 45.36 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.475 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02
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Xplor file |
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