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Yorodumi- PDB-3slp: Crystal Structure of Lambda Exonuclease in Complex with a 12 BP S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3slp | ||||||
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Title | Crystal Structure of Lambda Exonuclease in Complex with a 12 BP Symmetric DNA Duplex | ||||||
Components |
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Keywords | HYDROLASE/DNA / Type II Restriction Endonuclease Fold / 5'-3' dsDNA exonuclease / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information exodeoxyribonuclease (lambda-induced) / exonuclease activity / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage lambda (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Bell, C.E. / Zhang, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity. Authors: Zhang, J. / McCabe, K.A. / Bell, C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3slp.cif.gz | 176.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3slp.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 3slp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/3slp ftp://data.pdbj.org/pub/pdb/validation_reports/sl/3slp | HTTPS FTP |
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-Related structure data
Related structure data | 3sm4C 1avqS 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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1 |
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Unit cell |
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-Components
-Protein / DNA chain , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 26222.859 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: exo, red-alpha, redX / Production host: Escherichia coli (E. coli) References: UniProt: P03697, exodeoxyribonuclease (lambda-induced) #2: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 499 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #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: 2.6 Å3/Da / Density % sol: 52.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 22% PEG3350, 0.3 M sodium acetate, 0.1 M Tris, 5 mM calcium chloride, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97929 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 25, 2009 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.59 Å / Num. all: 32023 / Num. obs: 32023 / % possible obs: 87.12 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.3 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AVQ Resolution: 2.3→39.59 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.883 / SU B: 8.725 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.529 / ESU R Free: 0.309 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.527 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→39.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.361 Å / Total num. of bins used: 20
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