[English] 日本語
Yorodumi- PDB-1k6x: Crystal structure of Nmra, a negative transcriptional regulator i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k6x | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Nmra, a negative transcriptional regulator in complex with NAD at 1.5 A resolution (Trigonal form) | ||||||
Components | NmrA | ||||||
Keywords | TRANSCRIPTION / Rossmann fold transcriptional regulation short chain dehydrogenase reductase NADH binding | ||||||
Function / homology | Function and homology information 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 | Emericella nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Stammers, D.K. / Ren, J. / Leslie, K. / Nichols, C.E. / Lamb, H.K. / Cocklin, S. / Dodds, A. / Hawkins, A.R. | ||||||
Citation | Journal: EMBO J. / Year: 2002 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 crystallisation 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 |
| ||||||
Remark 999 | SEQUENCE BASED ON SEQUENCE BOTH GENOMIC DNA AND CDNA SHOWED ARG 238 MOST LIKELY THERE IS AN ERROR ...SEQUENCE BASED ON SEQUENCE BOTH GENOMIC DNA AND CDNA SHOWED ARG 238 MOST LIKELY THERE IS AN ERROR IN THE PUBLISHED SEQUENCE OR A SEQUENCE VARIANT IN THE STRAIN AS PER AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1k6x.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1k6x.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 1k6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k6x_validation.pdf.gz | 760.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1k6x_full_validation.pdf.gz | 767.2 KB | Display | |
Data in XML | 1k6x_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 1k6x_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/1k6x ftp://data.pdbj.org/pub/pdb/validation_reports/k6/1k6x | HTTPS FTP |
-Related structure data
Related structure data | 1k6iSC 1k6jC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 38835.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (mold) / Gene: nmrA / Plasmid: pTrc99a / Production host: Escherichia coli (E. coli) / Strain (production host): BL23 DE3 / References: UniProt: O59919, UniProt: Q5AU62*PLUS | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NAD / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: potassium chloride, sodium dihydrogen phosphate, potassium dihydrogen phosphate, MES, pH 6.5, 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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9919 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9919 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 54613 / % possible obs: 95 % / Observed criterion σ(I): -1.5 / Redundancy: 8.6 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3872 / % possible all: 68.4 |
Reflection shell | *PLUS % possible obs: 68.4 % / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K6I Resolution: 1.5→28.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1612646.17 / Data cutoff high rms absF: 1612646.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 78.6435 Å2 / ksol: 0.382178 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→28.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5.2 % / Rfactor obs: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.346 / Rfactor Rwork: 0.333 |