+Open data
-Basic information
Entry | Database: PDB / ID: 1x1y | ||||||
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Title | Water-mediate interaction at aprotein-protein interface | ||||||
Components |
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Keywords | HYDROLASE/PROTEIN BINDING / RNase-inhibitor complex / hydrolase/hydrolase inhibitor / HYDROLASE-PROTEIN BINDING COMPLEX | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus amyloliquefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ikura, T. / Urakubo, Y. / Ito, N. | ||||||
Citation | Journal: Chem.Phys. / Year: 2004 Title: Water-mediated interaction at a protein-protein interface Authors: Ikura, T. / Urakubo, Y. / Ito, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x1y.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x1y.ent.gz | 109.3 KB | Display | PDB format |
PDBx/mmJSON format | 1x1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x1y_validation.pdf.gz | 453.8 KB | Display | wwPDB validaton report |
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Full document | 1x1y_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | 1x1y_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 1x1y_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/1x1y ftp://data.pdbj.org/pub/pdb/validation_reports/x1/1x1y | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12341.670 Da / Num. of mol.: 3 / Mutation: Q2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: PML2BS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)[PLYSE] References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Protein | Mass: 10244.598 Da / Num. of mol.: 3 / Mutation: D35A, C40A, C82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: PML2BS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)[PLYSE] / References: UniProt: P11540 #3: 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: 2.52 Å3/Da / Density % sol: 51.26 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 9, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→51.3 Å / Num. all: 74419 / Num. obs: 74419 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.52 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.7→1.76 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→14.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 638688.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.8224 Å2 / ksol: 0.40042 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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