- PDB-4r8o: Crystal structure of a DUF3836 family protein (BVU_1206) from Bac... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 4r8o
Title
Crystal structure of a DUF3836 family protein (BVU_1206) from Bacteroides vulgatus ATCC 8482 at 2.50 A resolution
Components
Uncharacterized protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF12930 family (DUF3836) / single layer beta sheet protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Lipocalin - #720 / Protein of unknown function DUF3836 / Family of unknown function (DUF3836) / Lipocalin / Beta Barrel / Mainly Beta / Uncharacterized protein
Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 26-128 OF THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 4.91 Å3/Da / Density % sol: 74.94 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 25.0% Glycerol 1.50M ammonium sulfate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2014 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97905 Å / Relative weight: 1
Reflection twin
Crystal-ID
ID
Operator
Domain-ID
Fraction
1
1
H, K, L
1
0.499
1
1
-h,-k,l
2
0.501
Reflection
Resolution: 2.5→49.04 Å / Num. obs: 17436 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 9.79 % / Biso Wilson estimate: 84.846 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.06
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.5-2.57
8.92
2.439
0.75
11180
1254
98.3
2.57-2.64
1.099
1.7
12458
1225
99.6
2.64-2.71
0.744
2.6
12588
1223
99.7
2.71-2.8
0.577
3.3
11941
1163
99.7
2.8-2.89
0.522
3.6
11662
1155
99.7
2.89-2.99
0.349
5.4
10810
1092
99.7
2.99-3.1
0.297
6.6
10022
1061
99.8
3.1-3.23
0.182
10.5
9734
1023
98.9
3.23-3.37
0.115
16.7
10144
993
99.9
3.37-3.54
0.094
20.5
9574
944
99.8
3.54-3.73
0.078
25.2
9052
907
99.9
3.73-3.95
0.072
28.6
8334
851
100
3.95-4.23
0.065
31.1
7348
806
98.8
4.23-4.57
0.054
35.9
7718
766
99.9
4.57-5
0.052
36.8
6973
693
99.9
5-5.59
0.062
35.2
6080
632
99.7
5.59-6.46
0.068
32.8
4906
555
97.5
6.46-7.91
0.063
36.8
4869
490
99.8
7.91-11.18
0.056
37.8
3462
381
99
11.18-49.04
0.043
36.5
1870
222
95.3
-
Phasing
Phasing
Method: molecular replacement
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
PHASER
2.3.0
phasing
XSCALE
January10, 2014BUILT=20140307
datascaling
REFMAC
5.8.0073
refinement
XDS
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.04 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 10.521 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 4.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2444
881
5.1 %
RANDOM
Rwork
0.1768
-
-
-
obs
0.18
17387
99.13 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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