+Open data
-Basic information
Entry | Database: PDB / ID: 4bwm | ||||||
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Title | KlenTaq mutant in complex with a RNA/DNA hybrid | ||||||
Components |
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Keywords | TRANSFERASE/DNA/RNA / TRANSFERASE-DNA-RNA COMPLEX | ||||||
Function / homology | Function and homology information nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | THERMUS AQUATICUS (bacteria) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å | ||||||
Authors | Blatter, N. / Bergen, K. / Welte, W. / Diederichs, K. / Marx, A. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013 Title: Structure and Function of an RNA-Reading Thermostable DNA Polymerase. Authors: Blatter, N. / Bergen, K. / Nolte, O. / Welte, W. / Diederichs, K. / Mayer, J. / Wieland, M. / Marx, A. #1: Journal: Angew.Chem. / Year: 2013 Title: Struktur Und Funktion Einer RNA-Lesenden Thermostabilen DNA-Polymerase Authors: Blatter, N. / Bergen, K. / Nolte, O. / Welte, W. / Diederichs, K. / Mayer, J. / Wieland, M. / Marx, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bwm.cif.gz | 273.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bwm.ent.gz | 213.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bwm_validation.pdf.gz | 828.3 KB | Display | wwPDB validaton report |
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Full document | 4bwm_full_validation.pdf.gz | 831.1 KB | Display | |
Data in XML | 4bwm_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 4bwm_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/4bwm ftp://data.pdbj.org/pub/pdb/validation_reports/bw/4bwm | HTTPS FTP |
-Related structure data
Related structure data | 4bwjC 3rtvS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein / DNA chain / RNA chain , 3 types, 3 molecules ABG
#1: Protein | Mass: 61057.113 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT, RESIDUES 293-832 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Plasmid: PGDR11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19821, DNA-directed DNA polymerase |
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#2: DNA chain | Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#3: RNA chain | Mass: 5192.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 5 types, 641 molecules
#4: Chemical | ChemComp-DCT / | ||||||
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#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-FMT / #8: Water | ChemComp-HOH / | |
-Details
Sequence details | N-TERMINALLY |
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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: 3.21 Å3/Da / Density % sol: 61.7 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: HANGING DROP. 100MM TRIS PH8.5, 200MM MG-FORMATE, 20% PEG 8K MICROSEEDED |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2012 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→47.34 Å / Num. obs: 79729 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.59 % / Biso Wilson estimate: 26.55 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.73 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 6.62 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.7 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RTV Resolution: 1.749→47.985 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 19.98 / Stereochemistry target values: ML Details: RESIDUES 15 AND 16 OF THE TEMPLATE AND 1 AND 2 OF THE PRIMER ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.749→47.985 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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