- PDB-4fo5: Crystal structure of a thioredoxin-like protein (BDI_1100) from P... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 4fo5
Title
Crystal structure of a thioredoxin-like protein (BDI_1100) from Parabacteroides distasonis ATCC 8503 at 2.02 A resolution
Components
thioredoxin-like protein
Keywords
OXIDOREDUCTASE / AhpC/TSA family protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT (RESIDUES 25-166) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 25-166) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M sodium acetate, 30.0% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 2.02→29.869 Å / Num. obs: 8038 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.337 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.58
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.02-2.09
0.439
2.4
2596
1516
97.4
2.09-2.18
0.314
3.1
2792
1620
98.5
2.18-2.27
0.42
4.2
2762
1393
97.8
2.27-2.39
0.477
5.5
5092
1580
98.9
2.39-2.54
0.43
6.9
6212
1564
99.4
2.54-2.74
0.294
9.9
8380
1607
99.3
2.74-3.02
0.154
15.9
9117
1572
99.4
3.02-3.45
0.077
25.7
8919
1539
100
3.45-4.34
0.043
36.3
8983
1551
99.2
4.34
0.03
44.9
9074
1583
99.1
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SOLVE
phasing
XSCALE
December29, 2011
datascaling
BUSTER-TNT
2.10.0
refinement
XDS
datareduction
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.02→29.869 Å / Cor.coef. Fo:Fc: 0.9599 / Cor.coef. Fo:Fc free: 0.9504 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.CHLORIDE (CL) MODELED IN THE SOLVENT STRUCTURE IS PRESENT IN THE CRYSTALLIZATION CONDITION. 4.EXPERIMENTAL PHASES FROM MAD PHASING WERE USED AS RESTRAINTS DURING CRYSTALLOGRAPHIC REFINEMENT.
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