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Yorodumi- PDB-6d47: Crystal structure of a DNA polymerase III subunit beta DnaN slidi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d47 | ||||||
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Title | Crystal structure of a DNA polymerase III subunit beta DnaN sliding clamp from Mycobacterium marinum | ||||||
Components | Beta sliding clamp | ||||||
Keywords | DNA BINDING PROTEIN / NIAID / National Institute of Allergy and Infectious Disease / structural genomics / Mtb / griselimycin / tuberculosis / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium marinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of a DNA polymerase III subunit beta DnaN sliding clamp from Mycobacterium marinum Authors: Edwards, T.E. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d47.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d47.ent.gz | 128.6 KB | Display | PDB format |
PDBx/mmJSON format | 6d47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6d47_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 6d47_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 6d47_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6d47_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/6d47 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/6d47 | HTTPS FTP |
-Related structure data
Related structure data | 3p16S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43353.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria) Strain: ATCC BAA-535 / M / Gene: dnaN, MMAR_0002 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HI47 |
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#2: 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: 5.22 Å3/Da / Density % sol: 76.45 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MymaA.17987.a.B1.PW38239 at 22.54 mg/mL protein against Morpheus screen condition G6 = 10% PEG 8000, 20% EG, 0.02 M each carboxylic acid (sodium formate, ammonium acetate, trisodium citrate, ...Details: MymaA.17987.a.B1.PW38239 at 22.54 mg/mL protein against Morpheus screen condition G6 = 10% PEG 8000, 20% EG, 0.02 M each carboxylic acid (sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate), 0.1 M MOPS/HEPES pH 7.5, direct cryo, 290679g6, pcm7-8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→48.374 Å / Num. obs: 33494 / % possible obs: 99.8 % / Redundancy: 6.039 % / Biso Wilson estimate: 61.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Χ2: 1.069 / Net I/σ(I): 13.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3p16 Resolution: 2.45→48.374 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 171.64 Å2 / Biso mean: 75.4146 Å2 / Biso min: 38.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.45→48.374 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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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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