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Yorodumi- PDB-1ue6: Crystal structure of the single-stranded dna-binding protein from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ue6 | ||||||
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Title | Crystal structure of the single-stranded dna-binding protein from mycobacterium tuberculosis | ||||||
Components | Single-strand binding protein | ||||||
Keywords | DNA BINDING PROTEIN / OLIGONUCLEOTIDE BINDING FOLD / DNA-BINDING PROTEIN / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information nucleoid / single-stranded DNA binding / DNA replication / response to antibiotic / DNA damage response / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Saikrishnan, K. / Jeyakanthan, J. / Venkatesh, J. / Acharya, N. / Sekar, K. / Varshney, U. / Vijayan, M. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ue6.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ue6.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ue6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ue6_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
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Full document | 1ue6_full_validation.pdf.gz | 475.1 KB | Display | |
Data in XML | 1ue6_validation.xml.gz | 22 KB | Display | |
Data in CIF | 1ue6_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/1ue6 ftp://data.pdbj.org/pub/pdb/validation_reports/ue/1ue6 | HTTPS FTP |
-Related structure data
Related structure data | 1ue1SC 1ue5C 1ue7C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-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: 17372.066 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PET11d / Production host: Escherichia coli (E. coli) / References: UniProt: P0A610, UniProt: P9WGD5*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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