+Open data
-Basic information
Entry | Database: PDB / ID: 1m5r | ||||||
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Title | Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex | ||||||
Components |
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Keywords | TRANSFERASE/DNA / protein-dna complex / base-flipping / abasic site / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA beta-glucosyltransferase / DNA beta-glucosyltransferase activity / symbiont-mediated evasion of host restriction-modification system / DNA modification Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lariviere, L. / Morera, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: A Base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition state analog Authors: Lariviere, L. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m5r.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m5r.ent.gz | 155.7 KB | Display | PDB format |
PDBx/mmJSON format | 1m5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/1m5r ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m5r | HTTPS FTP |
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-Related structure data
Related structure data | 1ixyC 1jg6S 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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2 |
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Unit cell |
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-Components
-DNA chain , 2 types, 4 molecules CDEF
#1: DNA chain | Mass: 3890.550 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 3941.584 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 40719.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: BGT / Plasmid: pBSK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04547, DNA beta-glucosyltransferase |
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-Non-polymers , 4 types, 782 molecules
#4: Chemical | #5: Chemical | ChemComp-TRS / #6: Chemical | #7: 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: 2.36 Å3/Da / Density % sol: 47.94 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, tert-butanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Details: Lariviere, L., (2002) Acta Crystallogr., Sect.D, 58, 1484. | ||||||||||||||||||||||||||||||||||||||||
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 RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 84757 / Num. obs: 83161 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.068 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.4 / Num. unique all: 8025 / Rsym value: 0.422 / % possible all: 95.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.068 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JG6 Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |