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Yorodumi- PDB-1ljo: CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ljo | ||||||
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Title | CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION | ||||||
Components | Archaeal Sm-like protein AF-Sm2 | ||||||
Keywords | UNKNOWN FUNCTION / SNRNP / SM / CORE SNRNP DOMAIN / RNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.95 Å | ||||||
Authors | Toro, I. / Basquin, J. / Teo-Dreher, H. / Suck, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus. Authors: Toro, I. / Basquin, J. / Teo-Dreher, H. / Suck, D. #1: Journal: Embo J. / Year: 2001 Title: RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex. Authors: Toro, I. / Thore, S. / Mayer, C. / Basquin, J. / Sraphin, B. / Suck, D. | ||||||
History |
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Remark 600 | HETEROGEN Cd ion sitting on six-fold axis is modelling a sulphate ion |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ljo.cif.gz | 27.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ljo.ent.gz | 18 KB | Display | PDB format |
PDBx/mmJSON format | 1ljo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ljo_validation.pdf.gz | 439.5 KB | Display | wwPDB validaton report |
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Full document | 1ljo_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 1ljo_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1ljo_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/1ljo ftp://data.pdbj.org/pub/pdb/validation_reports/lj/1ljo | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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Details | The biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: -Y,X-Y,Z; Y-X,-X,Z; -X,-Y,Z; Y,Y-X,Z and X-Y,X,Z |
-Components
#1: Protein | Mass: 8617.045 Da / Num. of mol.: 1 / Mutation: 'N-terminal GA added' Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0362 / Plasmid: modified pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29885 | ||
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#2: Chemical | ChemComp-CD / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.92 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: ammonium sulphate, lithium sulphate, sodium sulphate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.3 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.95→27.1 Å / Num. all: 4522 / Num. obs: 4522 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 18.567 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 10.5 | ||||||||||||||||||
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 2 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 4.2 / Num. unique all: 598 / Rsym value: 0.173 / % possible all: 90.9 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 11984 / Rmerge(I) obs: 0.051 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 90.9 % / Rmerge(I) obs: 0.173 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: Built by ARP/WARP (68 residues) Resolution: 1.95→27.1 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKELIHOOD TARGET
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Solvent computation | Solvent model: flat model / Bsol: 56.1311 Å2 / ksol: 0.379594 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→27.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor all: 0.195 / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.194 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.294 / Rfactor Rwork: 0.199 |