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Yorodumi- PDB-2xca: TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xca | ||||||
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Title | TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dGTP - MAGNESIUM FORM | ||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / TRANSLESION NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | Function and homology information error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Irimia, A. / Egli, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus Authors: Irimia, A. / Loukachevitch, L.V. / Eoff, R.L. / Guengerich, F.P. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xca.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xca.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 2xca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xca_validation.pdf.gz | 786.7 KB | Display | wwPDB validaton report |
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Full document | 2xca_full_validation.pdf.gz | 798.4 KB | Display | |
Data in XML | 2xca_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 2xca_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/2xca ftp://data.pdbj.org/pub/pdb/validation_reports/xc/2xca | HTTPS FTP |
-Related structure data
Related structure data | 2xc9C 2xcpC 2c22S 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41086.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Gene: DPO4 / Plasmid: PET22B/DPO4-NHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules PT
#2: DNA chain | Mass: 4080.671 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 5388.480 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 197 molecules
#4: Chemical | ChemComp-DGT / | ||
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#5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE N-TERMINAL 6 RESIDUES HIS TAG ARE DISORDERED AND MISSING FROM THE STRUCTURE. THE C-TERMINAL 11 ...THE N-TERMINAL 6 RESIDUES HIS TAG ARE DISORDERED |
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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: 3.23 Å3/Da / Density % sol: 50.09 % Description: THE MODEL POSITION WAS OPTIMIZED BY SEVERAL ROUNDS OF RIGID BODY REFINEMENT. |
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Crystal grow | pH: 7.5 Details: RESERVOIR: 12-20% POLYETHYLENE GLYCOL 3350, 0.2 M AMMONIUM ACETATE, 0.1 M MAGNESIUM ACETATE, 20 MM TRIS (PH 7.5) DROP: 10MM TRIS-CL PH 7.5, 30 MM NACL, 0.5MM DGTP, 2.5MM MGCL2, 6-10% ...Details: RESERVOIR: 12-20% POLYETHYLENE GLYCOL 3350, 0.2 M AMMONIUM ACETATE, 0.1 M MAGNESIUM ACETATE, 20 MM TRIS (PH 7.5) DROP: 10MM TRIS-CL PH 7.5, 30 MM NACL, 0.5MM DGTP, 2.5MM MGCL2, 6-10% POLYETHYLENE GLYCOL 3350 0.1M AMMONIUM ACETATE, 0.05M MAGNESIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.13 Å / Num. obs: 18457 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C22 Resolution: 2.5→29.13 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1064868.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.5208 Å2 / ksol: 0.360388 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.13 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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