- PDB-1l9g: CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM T. MARITIMA -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 1l9g
Title
CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM T. MARITIMA
Components
Conserved hypothetical protein
Keywords
HYDROLASE / DNA Glycosylase / Base excision repair / Uracil / Thermophile / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information
uracil-DNA glycosylase / uracil DNA N-glycosylase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding Similarity search - Function
Resolution: 2.5→2.59 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 8.3 / Num. unique all: 822 / Rsym value: 0.278 / % possible all: 100
-
Processing
Software
Name
Classification
MAR345
datacollection
SCALEPACK
datascaling
MLPHARE
phasing
CNS
refinement
Refinement
Method to determine structure: SAD / Resolution: 2.5→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Freidel pairs treated separate while counting reflections. The C-terminal residue Gly192 is missing in the density.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2808
745
-
RANDOM
Rwork
0.226
-
-
-
all
0.231
15070
-
-
obs
0.231
15070
96.5 %
-
Refinement step
Cycle: LAST / Resolution: 2.5→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1497
0
13
65
1575
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.019
X-RAY DIFFRACTION
c_angle_deg
1.8
X-RAY DIFFRACTION
c_dihedral_angle_d
24.6
+
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