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Yorodumi- PDB-2g4c: Crystal Structure of human DNA polymerase gamma accessory subunit -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g4c | ||||||
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Title | Crystal Structure of human DNA polymerase gamma accessory subunit | ||||||
Components | DNA polymerase gamma subunit 2 | ||||||
Keywords | TRANSFERASE / alpha and beta protein / anti-codon binding domain-like / aaRS class II-like | ||||||
Function / homology | Function and homology information gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / mitochondrial nucleoid / DNA polymerase binding / Transcriptional activation of mitochondrial biogenesis / DNA-templated DNA replication / double-stranded DNA binding / in utero embryonic development ...gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / mitochondrial nucleoid / DNA polymerase binding / Transcriptional activation of mitochondrial biogenesis / DNA-templated DNA replication / double-stranded DNA binding / in utero embryonic development / DNA-directed DNA polymerase activity / mitochondrial matrix / mitochondrion / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Fan, L. / Farr, C.L. / Kaguni, L.S. / Tainer, J.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase Authors: Fan, L. / Kim, S. / Farr, C.L. / Schaefer, K.T. / Randolph, K.M. / Tainer, J.A. / Kaguni, L.S. | ||||||
History |
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Remark 999 | SEQUENCE Residue 169 is a Thr according to Carrodeguas and Bogenhagen, 2000, Nucleic Acids Res. 28, ...SEQUENCE Residue 169 is a Thr according to Carrodeguas and Bogenhagen, 2000, Nucleic Acids Res. 28, 1237-1244. The sequence in the deposition agrees with the reference |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g4c.cif.gz | 299.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g4c.ent.gz | 243.7 KB | Display | PDB format |
PDBx/mmJSON format | 2g4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g4c_validation.pdf.gz | 472.6 KB | Display | wwPDB validaton report |
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Full document | 2g4c_full_validation.pdf.gz | 577.1 KB | Display | |
Data in XML | 2g4c_validation.xml.gz | 68.7 KB | Display | |
Data in CIF | 2g4c_validation.cif.gz | 90.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/2g4c ftp://data.pdbj.org/pub/pdb/validation_reports/g4/2g4c | HTTPS FTP |
-Related structure data
Related structure data | 1g5hS 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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2 |
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Unit cell |
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Details | The biological assembly is likely a homodimer. |
-Components
#1: Protein | Mass: 53907.449 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLG2, MTPOLB / Plasmid: pQESL-Hp55 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UHN1, DNA-directed DNA polymerase #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: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 10%PEG 8000, 100 mM Tris-Cl, pH 8.0, VAPOR DIFFUSION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2004 |
Radiation | Monochromator: Si(iii) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→50 Å / Num. all: 34088 / Num. obs: 33633 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 3.15→3.26 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 1.94 / Num. unique all: 3386 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G5H Resolution: 3.15→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.15→50 Å
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Refine LS restraints |
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Xplor file |
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