+Open data
-Basic information
Entry | Database: PDB / ID: 1npr | ||||||
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Title | CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS NUSG IN C222(1) | ||||||
Components | Transcription antitermination protein nusG | ||||||
Keywords | TRANSCRIPTION / Transcription factor / NusG | ||||||
Function / homology | Function and homology information transcription elongation-coupled chromatin remodeling / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / cytosol Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Knowlton, J.R. / Bubunenko, M. / Andrykovitch, M. / Guo, W. / Routzhan, K.M. / Waugh, D.S. / Court, D.L. / Ji, X. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: A Spring-Loaded State of NusG in Its Functional Cycle Is Suggested by X-ray Crystallography and Supported by Site-Directed Mutants Authors: Knowlton, J.R. / Bubunenko, M. / Andrykovitch, M. / Guo, W. / Routzhan, K.M. / Waugh, D.S. / Court, D.L. / Ji, X. #1: Journal: Embo J. / Year: 2002 Title: Crystal structures of transcription factor NusG in light of its nucleic acid-and protein-binding activities Authors: Steiner, T. / Kaiser, J.T. / Marinkovic, S. / Huber, R. / Wahl, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1npr.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1npr.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 1npr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1npr_validation.pdf.gz | 424.1 KB | Display | wwPDB validaton report |
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Full document | 1npr_full_validation.pdf.gz | 432.3 KB | Display | |
Data in XML | 1npr_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1npr_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1npr ftp://data.pdbj.org/pub/pdb/validation_reports/np/1npr | HTTPS FTP |
-Related structure data
Related structure data | 1nppSC 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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Unit cell |
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-Components
#1: Protein | Mass: 28041.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: NUSG OR AQ_1931 / Plasmid: pKM702 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O67757 |
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#2: 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: 3.06 Å3/Da / Density % sol: 59.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 4000 Hepes Glycerol Isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging dropDetails: Andrykovitch, M., (2002) Acta Crystallogr., D58, 2157. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 15, 2000 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→29.19 Å / Num. all: 17608 / Num. obs: 16961 / % possible obs: 96.3 % / Observed criterion σ(I): -2 / Redundancy: 3.8 % / Biso Wilson estimate: 45.2 Å2 / Limit h max: 29 / Limit h min: 0 / Limit k max: 56 / Limit k min: 0 / Limit l max: 36 / Limit l min: 0 / Observed criterion F max: 836060.11 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.058 / Rsym value: 0.043 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.21→2.26 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.9 / Num. unique all: 719 / Rsym value: 0.456 / % possible all: 85.2 |
Reflection | *PLUS Highest resolution: 2.22 Å / Lowest resolution: 35 Å / Redundancy: 4.11 % |
Reflection shell | *PLUS Highest resolution: 2.22 Å / % possible obs: 85.2 % / Mean I/σ(I) obs: 1.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1NPP Resolution: 2.21→29.19 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 61.3083 Å2 / ksol: 0.333095 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.8 Å2 / Biso mean: 62.97 Å2 / Biso min: 25.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.21→29.19 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.22 Å / Lowest resolution: 35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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