+Open data
-Basic information
Entry | Database: PDB / ID: 4a1n | ||||||
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Title | Human Mitochondrial endo-exonuclease | ||||||
Components | NUCLEASE EXOG, MITOCHONDRIAL | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / mitochondrial inner membrane / nucleic acid binding / protein-containing complex / mitochondrion ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / mitochondrial inner membrane / nucleic acid binding / protein-containing complex / mitochondrion / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Welin, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Graslund, S. / Hammarstrom, M. ...Welin, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nyman, T. / Persson, C. / Schuler, H. / Thorsell, A.G. / Tresaugues, L. / Weigelt, J. / Nordlund, P. | ||||||
Citation | Journal: To be Published Title: Human Mitochondrial Endo-Exonuclease Authors: Welin, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, ...Authors: Welin, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nyman, T. / Persson, C. / Schuler, H. / Thorsell, A.G. / Tresaugues, L. / Weigelt, J. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a1n.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a1n.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/4a1n ftp://data.pdbj.org/pub/pdb/validation_reports/a1/4a1n | HTTPS FTP |
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-Related structure data
Related structure data | 3ismS 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
#1: Protein | Mass: 37981.941 Da / Num. of mol.: 1 / Fragment: RESIDUES 42-368 Source method: isolated from a genetically manipulated source Details: CLONING ARTIFACT GLU330VAL / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CH2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE References: UniProt: Q9Y2C4, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters | ||||||
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#2: Chemical | ChemComp-MG / | ||||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Sequence details | THERE IS A GLU330VAL MUTATION IN THE PROTEIN SEQUENCE. THE SIDE CHAIN WAS NOT VISIBLE IN THE ...THERE IS A GLU330VAL MUTATION IN THE PROTEIN SEQUENCE. THE SIDE CHAIN WAS NOT VISIBLE IN THE ELECTRON DENSITY. WE BELIEVE THIS IS A CLONING ARTIFACT. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.76 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→44.7 Å / Num. obs: 13052 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 51.36 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ISM Resolution: 2.8→44.68 Å / Cor.coef. Fo:Fc: 0.9278 / Cor.coef. Fo:Fc free: 0.8949 / SU R Cruickshank DPI: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.411 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.268 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CL NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2375. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=2. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CL NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2375. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=2. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
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Displacement parameters | Biso mean: 37.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.283 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→44.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→3.02 Å / Total num. of bins used: 7
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