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- PDB-1k6j: Crystal structure of Nmra, a negative transcriptional regulator (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k6j | ||||||
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Title | Crystal structure of Nmra, a negative transcriptional regulator (Monoclinic form) | ||||||
![]() | NmrA | ||||||
![]() | TRANSCRIPTION / Rossmann fold transcriptional regulation short chain dehydrogenase reductase | ||||||
Function / homology | ![]() nitrogen catabolite repression of transcription from RNA polymerase II promoter / nitrogen catabolite repression of transcription / regulation of nitrogen utilization / NADP+ binding / NAD+ binding / NAD binding / oxidoreductase activity / negative regulation of DNA-templated transcription / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stammers, D.K. / Ren, J. / Leslie, K. / Nichols, C.E. / Lamb, H.K. / Cocklin, S. / Dodds, A. / Hawkins, A.R. | ||||||
![]() | ![]() Title: The structure of the negative transcriptional regulator NmrA reveals a structural superfamily which includes the short-chain dehydrogenase/reductases. Authors: Stammers, D.K. / Ren, J. / Leslie, K. / Nichols, C.E. / Lamb, H.K. / Cocklin, S. / Dodds, A. / Hawkins, A.R. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Expression, purification and crystallization of Aspergillus nidulans NmrA, a negative regulatory protein involved in nitrogen-metabolite repression. Authors: Nichols, C.E. / Cocklin, S. / Dodds, A. / Ren, J. / Lamb, H. / Hawkins, A.R. / Stammers, D.K. | ||||||
History |
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Remark 999 | BASED ON SEQUENCE BOTH GENOMIC DNA AND CDNA SHOWED ARG 238 ON CHAINS A AND B. MOST LIKELY THERE IS ... BASED ON SEQUENCE BOTH GENOMIC DNA AND CDNA SHOWED ARG 238 ON CHAINS A AND B. MOST LIKELY THERE IS AN ERROR IN THE PUBLISHED SEQUENCE OR A SEQUENCE VARIANT IN THE STRAIN USED |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161 KB | Display | ![]() |
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PDB format | ![]() | 124.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
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Full document | ![]() | 450.6 KB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 52.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k6iSC ![]() 1k6xC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38835.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.32 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: sodium chloride, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Nichols, C.E., (2001) Acta Crystallogr., Sect.D, 57, 1722. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Sep 23, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 78344 / % possible obs: 95.5 % / Observed criterion σ(I): -1.5 / Redundancy: 5.2 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 1.3 / Num. unique all: 5966 / % possible all: 73.3 |
Reflection | *PLUS Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 73.3 % / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1K6I Resolution: 1.8→19.94 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2110594.76 / Data cutoff high rms absF: 2110594.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.3882 Å2 / ksol: 0.400001 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 5.3 % / Rfactor Rwork: 0.285 |