+Open data
-Basic information
Entry | Database: PDB / ID: 2bhn | ||||||
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Title | XPF from Aeropyrum pernix | ||||||
Components | XPF ENDONUCLEASE | ||||||
Keywords | HYDROLASE / STRUCTURE SPECIFIC ENDONUCLEASE / NUCLEOTIDE EXCISION REPAIR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Newman, M. / Murray-Rust, J. / Lally, J. / Rudolf, J. / Fadden, A. / Knowles, P.P. / White, M.F. / McDonald, N.Q. | ||||||
Citation | Journal: EMBO J. / Year: 2005 Title: Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition. Authors: Newman, M. / Murray-Rust, J. / Lally, J. / Rudolf, J. / Fadden, A. / Knowles, P.P. / White, M.F. / McDonald, N.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bhn.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bhn.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/2bhn ftp://data.pdbj.org/pub/pdb/validation_reports/bh/2bhn | HTTPS FTP |
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-Related structure data
Related structure data | 2bgwSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 6
NCS oper:
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-Components
#1: Protein | Mass: 24551.436 Da / Num. of mol.: 4 / Fragment: 19-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) Description: A PERNIX GENOME SEQUENCING PROJECT GNE APE 1436, ACCESSION CODE C72622 Plasmid: PET-14B-3C / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA/PLYSS References: UniProt: Q9YC15, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases Sequence details | RESIDUES 19-231 ONLY | |
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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: 2.32 Å3/Da / Density % sol: 47 % Description: SOLUTION CHECKED BY CROSS-PHASING OF AN OSMATE DERIVATIVE |
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Crystal grow | Method: vapor diffusion, sitting drop / Details: 65% V/V MPD, 0.1M TRIS-HCL PH8.0. SITTING DROPS. |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→38.93 Å / Num. obs: 52273 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SEPARATE DOMAINS FROM PART-REFINED PDB ENTRY 2BGW Resolution: 3.2→25 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.836 / SU B: 62.516 / SU ML: 0.535 / Cross valid method: THROUGHOUT / ESU R Free: 0.663 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.83 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→25 Å
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Refine LS restraints |
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