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- PDB-1ue6: Crystal structure of the single-stranded dna-binding protein from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ue6 | ||||||
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Title | Crystal structure of the single-stranded dna-binding protein from mycobacterium tuberculosis | ||||||
![]() | Single-strand binding protein | ||||||
![]() | DNA BINDING PROTEIN / OLIGONUCLEOTIDE BINDING FOLD / DNA-BINDING PROTEIN / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | ![]() nucleoid / single-stranded DNA binding / DNA replication / response to antibiotic / DNA damage response / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Saikrishnan, K. / Jeyakanthan, J. / Venkatesh, J. / Acharya, N. / Sekar, K. / Varshney, U. / Vijayan, M. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications Authors: Saikrishnan, K. / Jeyakanthan, J. / Venkatesh, J. / Acharya, N. / Sekar, K. / Varshney, U. / Vijayan, M. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2002 Title: Crystallization and preliminary X-ray studies of the single-stranded DNA-binding protein from Mycobacterium tuberculosis. Authors: Saikrishnan, K. / Jeyakanthan, J. / Venkatesh, J. / Acharya, N. / Purnapatre, K. / Sekar, K. / Varshney, U. / Vijayan, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98 KB | Display | ![]() |
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PDB format | ![]() | 74.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ue1SC ![]() 1ue5C ![]() 1ue7C S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17372.066 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 2M MAGNESIUM CHLORIDE, 500mM SODIUM CHLORIDE, 20mM TRIS-HCL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Saikrishnan, K., (2002) Acta Cryst., D58, 327. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 30, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 75505 / Num. obs: 17174 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 97.6 |
Reflection | *PLUS Highest resolution: 2.7 Å / Redundancy: 4.4 % |
Reflection shell | *PLUS % possible obs: 97.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.582 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UE1 Resolution: 2.7→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 205124.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: A LARGE NUMBER OF THE ISOLATED WATER MOLECULES REPRESENT THE DISCREET AND ISOLATED ELECTRON DENSITIES, WHICH MAY CORRESPOND TO THE UNDEFINED REGIONS OF THE POLYPEPTIDE CHAIN PRIMARILY AT THE ...Details: A LARGE NUMBER OF THE ISOLATED WATER MOLECULES REPRESENT THE DISCREET AND ISOLATED ELECTRON DENSITIES, WHICH MAY CORRESPOND TO THE UNDEFINED REGIONS OF THE POLYPEPTIDE CHAIN PRIMARILY AT THE C-TERMINUS AND THE LOOPS. The crystals were obtained from a sample containing truncated protein. the nature of the truncation is not known.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.224 Å2 / ksol: 0.290218 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 15 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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