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- PDB-2pua: CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pua | ||||||
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Title | CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES | ||||||
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![]() | TRANSCRIPTION/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / DNA-BINDING REGULATORY PROTEIN / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() guanine binding / negative regulation of purine nucleotide biosynthetic process / purine nucleotide biosynthetic process / DNA-binding transcription repressor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() | ||||||
![]() | Schumacher, R.G. / Choi, K.Y. / Zalkin, H. / Brennan, M.A. | ||||||
![]() | ![]() Title: Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. Authors: Schumacher, M.A. / Choi, K.Y. / Zalkin, H. / Brennan, R.G. #1: ![]() Title: Structure-Based Redesign of Corepressor Specificity of the Escherichia Coli Purine Repressor by Substitution of Residue 190 Authors: Lu, F. / Schumacher, M.A. / Arvidson, D.N. / Haldimann, A. / Wanner, B.L. / Zalkin, H. / Brennan, R.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.7 KB | Display | ![]() |
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PDB format | ![]() | 66.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | THE COMPLEX LIES ON A CRYSTALLOGRAPHIC TWO-FOLD AXIS, AND ONLY ONE MONOMER-DNA HALF-SITE CONSTITUTES THE ASYMMETRIC UNIT. THE COORDINATES COMPRISE ONE REPRESSOR MONOMER AND ONE DNA STRAND FOR THE ENTIRE SITE. THE FULL COMPLEX CAN BE CONSTRUCTED BY GENERATING THE SECOND HALF USING THE CRYSTALLOGRAPHIC SYMMETRY OPERATION (X, -Y, -Z). |
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Components
#1: DNA chain | Mass: 5202.384 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (synth.) synthetic construct (others) |
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#2: Protein | Mass: 38005.480 Da / Num. of mol.: 1 / Mutation: R190A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-6MP / |
#4: Water | ChemComp-HOH / |
Compound details | THE HYDROGEN BONDS FROM ARG 190 TO THE O6 EXOCYCLIC ATOM IS WHAT DETERMINES PURR'S SPECIFICITY FOR ...THE HYDROGEN BONDS FROM ARG 190 TO THE O6 EXOCYCLIC ATOM IS WHAT DETERMINES |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Details: Schumacher, M.A., (1994) J.Mol.Biol, 242, 302. / pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.9 Å / Num. obs: 14911 / % possible obs: 99 % / Redundancy: 3.43 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.7 |
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Processing
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Refinement | Resolution: 2.9→10 Å / Isotropic thermal model: ISOTROPIC / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 10 Å / Num. reflection all: 18818 / σ(F): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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