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Yorodumi- PDB-4z1z: Crystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z1z | ||||||
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Title | Crystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable DNA with a TTCT Central Four | ||||||
Components |
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Keywords | hydrolase/dna / Hydrolase-DNA complex / LAGLIDADG / homing endonuclease / meganuclease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sordaria macrospora (fungus) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Hallinan, J.P. / Stoddard, B.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2016 Title: Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity. Authors: Lambert, A.R. / Hallinan, J.P. / Shen, B.W. / Chik, J.K. / Bolduc, J.M. / Kulshina, N. / Robins, L.I. / Kaiser, B.K. / Jarjour, J. / Havens, K. / Scharenberg, A.M. / Stoddard, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z1z.cif.gz | 186.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z1z.ent.gz | 139.7 KB | Display | PDB format |
PDBx/mmJSON format | 4z1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z1z_validation.pdf.gz | 479.3 KB | Display | wwPDB validaton report |
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Full document | 4z1z_full_validation.pdf.gz | 507.8 KB | Display | |
Data in XML | 4z1z_validation.xml.gz | 29 KB | Display | |
Data in CIF | 4z1z_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/4z1z ftp://data.pdbj.org/pub/pdb/validation_reports/z1/4z1z | HTTPS FTP |
-Related structure data
Related structure data | 4yhxC 4yisC 4yitC 4z20C 5espC 4loxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34283.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell) (fungus) Strain: ATCC MYA-333 / DSM 997 / K(L3346) / K-hell / Gene: SMAC_12671 / Production host: Escherichia coli (E. coli) / References: UniProt: F7WD42 |
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-DNA chain , 2 types, 4 molecules DFCE
#2: DNA chain | Mass: 8412.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 8799.677 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 12 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3550, 5mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.55 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.55 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→50 Å / Num. obs: 16992 / % possible obs: 98.5 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.061 / Rrim(I) all: 0.229 / Χ2: 1.164 / Net I/av σ(I): 13 / Net I/σ(I): 5.1 / Num. measured all: 234481 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LOX Resolution: 3.2→89.64 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.876 / SU B: 36.501 / SU ML: 0.595 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.622 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 123.17 Å2 / Biso mean: 44.818 Å2 / Biso min: 8.4 Å2
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Refinement step | Cycle: final / Resolution: 3.2→89.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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