+Open data
-Basic information
Entry | Database: PDB / ID: 2b34 | ||||||
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Title | Structure of MAR1 Ribonuclease from Caenorhabditis elegans | ||||||
Components | MAR1 Ribonuclease | ||||||
Keywords | HYDROLASE / Isochorismatase Family / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / cytoplasm / Alpha Beta / Isochorismatase domain-containing protein Function and homology information | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.141 Å | ||||||
Authors | Schormann, N. / Karpova, E. / Li, S. / Symersky, J. / Zhang, Y. / Lu, S. / Zhou, Q. / Lin, G. / Cao, Z. / Luo, M. ...Schormann, N. / Karpova, E. / Li, S. / Symersky, J. / Zhang, Y. / Lu, S. / Zhou, Q. / Lin, G. / Cao, Z. / Luo, M. / Qiu, S. / Luan, C.-H. / Luo, D. / Huang, W. / Shang, Q. / McKinstry, A. / An, J. / Tsao, J. / Carson, M. / Stinnett, M. / Chen, Y. / Johnson, D. / Gary, R. / Arabshahi, A. / Bunzel, R. / Bray, T. / DeLucas, L. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: To be Published Title: Structure of MAR1 Ribonuclease from Caenorhabditis elegans Authors: Schormann, N. / Karpova, E. / Li, S. / Symersky, J. / Zhang, Y. / Lu, S. / Zhou, Q. / Lin, G. / Cao, Z. / Luo, M. / Qiu, S. / Luan, C.-H. / Luo, D. / Huang, W. / Shang, Q. / McKinstry, A. / ...Authors: Schormann, N. / Karpova, E. / Li, S. / Symersky, J. / Zhang, Y. / Lu, S. / Zhou, Q. / Lin, G. / Cao, Z. / Luo, M. / Qiu, S. / Luan, C.-H. / Luo, D. / Huang, W. / Shang, Q. / McKinstry, A. / An, J. / Tsao, J. / Carson, M. / Stinnett, M. / Chen, Y. / Johnson, D. / Gary, R. / Arabshahi, A. / Bunzel, R. / Bray, T. / DeLucas, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b34.cif.gz | 302.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b34.ent.gz | 248.6 KB | Display | PDB format |
PDBx/mmJSON format | 2b34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b34_validation.pdf.gz | 470.2 KB | Display | wwPDB validaton report |
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Full document | 2b34_full_validation.pdf.gz | 489.8 KB | Display | |
Data in XML | 2b34_validation.xml.gz | 58.4 KB | Display | |
Data in CIF | 2b34_validation.cif.gz | 82.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/2b34 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/2b34 | HTTPS FTP |
-Related structure data
Related structure data | 1x9gS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The asymmetric unit contains two tetramers in an octameric assembly, with the second tetramer off-center of the first. The biological unit is probably the tetramer. |
-Components
#1: Protein | Mass: 21877.426 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI / References: UniProt: Q20062 #2: 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: 2.2 Å3/Da / Density % sol: 44.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG3350, 0.2M sodium acetate, 0.1M Tris , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2005 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→50 Å / Num. all: 84631 / Num. obs: 84631 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.14→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.168 / Num. unique all: 8022 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The starting model was created by the Swiss-Model Server based on PDB entry 1X9G using the C. elegans target sequence (F35G2.2) Resolution: 2.141→41.67 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.843 / SU ML: 0.157 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.23 / 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: 25.126 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.141→41.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.141→2.196 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 20
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