+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ra4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Methanococcus jannaschii L7Ae protein | ||||||
![]() | 50S ribosomal protein L7Ae | ||||||
![]() | STRUCTURAL PROTEIN / alpha-beta-alpha sandwich fold | ||||||
Function / homology | ![]() box C/D sno(s)RNA binding / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / box C/D snoRNP assembly / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / cytosolic large ribosomal subunit ...box C/D sno(s)RNA binding / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / box C/D snoRNP assembly / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Suryadi, J. / Tran, E.J. / Maxwell, E.S. / Brown, B.A. | ||||||
![]() | ![]() Title: The crystal structure of the Methanocaldococcus jannaschii multifunctional L7Ae RNA-binding protein reveals an induced-fit interaction with the box C/D RNAs. Authors: Suryadi, J. / Tran, E.J. / Maxwell, E.S. / Brown, B.A. #1: ![]() Title: Efficient RNA 2'-O-methylation requires juxaposed and symmetrically assembled archaeal box C/D and C'/D' RNPs Authors: Tran, E.J. / Zhang, X. / Maxwell, E.S. #2: ![]() Title: Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein Authors: Kuhn, J.F. / Tran, E.J. / Maxwell, E.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 40.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 26.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 431.8 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 13.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xbiC ![]() 1ck2S ![]() 1e7kS ![]() 1jj2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12986.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RPL7AE, MJ1203 / Plasmid: pET28a / Production host: ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.83 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 % PEG 4000, 10 % isopropanol, 100 mM HEPES-NaOH, pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 5, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→35.17 Å / Num. obs: 9674 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.86→1.98 Å / Mean I/σ(I) obs: 12.97 / Num. unique all: 1434 / Rsym value: 0.151 / % possible all: 96.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Threaded model created in SWISS PROT using a composite of the following PDB Entries: 1E7K 1CK2 1JJ2 MOL_ID 8; CHAIN: F Resolution: 1.86→35.17 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 486425.75 / Data cutoff high rms absF: 486425.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.7497 Å2 / ksol: 0.41016 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.1 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→35.17 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|