- PDB-2ov7: The first domain of the ribosomal protein L1 from Thermus thermophilus -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2ov7
Title
The first domain of the ribosomal protein L1 from Thermus thermophilus
Components
50S ribosomal protein L1
Keywords
RIBOSOMAL PROTEIN / ribosomal protein L1 / Thermus thermophilus
Function / homology
Function and homology information
regulation of translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation Similarity search - Function
50S ribosomal protein L1; Chain A, Domain 1 / Arc Repressor Mutant, subunit A / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family ...50S ribosomal protein L1; Chain A, Domain 1 / Arc Repressor Mutant, subunit A / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Helix non-globular / Special Similarity search - Domain/homology
Resolution: 2.3→2.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1782 / Rsym value: 0.461 / % possible all: 98.4
-
Processing
Software
Name
Version
Classification
PHASER
phasing
CNS
1.1
refinement
XDS
datareduction
XSCALE
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: The first domain of L1 from Thermus thermophilus Resolution: 2.3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: twin_lsq Details: The data were twinned with the twinning operator= h+k,-k,-l and twinning fraction= 0.41.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2328
1354
-
RANDOM
Rwork
0.1927
-
-
-
all
-
14797
-
-
obs
-
14468
98.7 %
-
Displacement parameters
Biso mean: 60.7 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.475 Å2
-3.17 Å2
0 Å2
2-
-
-1.475 Å2
0 Å2
3-
-
-
2.95 Å2
Refine analyze
Luzzati coordinate error obs: 0.26 Å
Refinement step
Cycle: LAST / Resolution: 2.3→15 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3076
0
0
152
3228
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.006
X-RAY DIFFRACTION
c_angle_deg
0.804
X-RAY DIFFRACTION
c_dihedral_angle_d
24.9
X-RAY DIFFRACTION
c_improper_angle_d
1.24
LS refinement shell
Resolution: 2.3→2.4 Å
Rfactor
Num. reflection
% reflection
Rfree
0.2339
168
-
Rwork
0.2099
-
-
obs
-
1658
100 %
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi