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Yorodumi- PDB-4fm1: Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in ed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fm1 | ||||||
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Title | Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase / DNA binding / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Gouge, J. / Delarue, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase. Authors: Gouge, J. / Ralec, C. / Henneke, G. / Delarue, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fm1.cif.gz | 348.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fm1.ent.gz | 274.7 KB | Display | PDB format |
PDBx/mmJSON format | 4fm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fm1_validation.pdf.gz | 460.9 KB | Display | wwPDB validaton report |
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Full document | 4fm1_full_validation.pdf.gz | 467.8 KB | Display | |
Data in XML | 4fm1_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 4fm1_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/4fm1 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/4fm1 | HTTPS FTP |
-Related structure data
Related structure data | 4fltC 4fluC 4flvC 4flwSC 4flxC 4flyC 4flzC 4fm0C 4fm2C 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 , 1 types, 1 molecules A
#1: Protein | Mass: 91809.938 Da / Num. of mol.: 1 / Mutation: D215A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Orsay / Gene: polI, pol, PYRAB17200, PAB1128 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CL77, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules PT
#2: DNA chain | Mass: 2411.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4008.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 260 molecules
#4: Chemical | ChemComp-GOL / | ||
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#5: Chemical | ChemComp-MES / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 7-12% PEG 20000, 100 mM MES pH 6.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.89231 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2010 |
Radiation | Monochromator: channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.89231 Å / Relative weight: 1 |
Reflection | Resolution: 3→44.01 Å / Num. all: 505777 / % possible obs: 92.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 59.7 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2844 / Rsym value: 0.38 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FLW Resolution: 3→44.01 Å / Cor.coef. Fo:Fc: 0.9175 / Cor.coef. Fo:Fc free: 0.861 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.313 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→44.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.16 Å / Total num. of bins used: 10
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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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