- PDB-4zys: Crystal structure of an exotoxin 6 (SAV0422) from Staphylococcus ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4zys
Title
Crystal structure of an exotoxin 6 (SAV0422) from Staphylococcus aureus subsp. aureus Mu50 at 2.25 A resolution
Components
exotoxin 6
Keywords
SUGAR BINDING PROTEIN / exotoxin / superantigen-like protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (31-226) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (31-226) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.18 Å3/Da / Density % sol: 43.68 %
Resolution: 2.25→29.328 Å / Num. obs: 19266 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 1.921 % / Biso Wilson estimate: 31.574 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.124 / Net I/σ(I): 7.14 / Num. measured all: 67264
Reflection shell
Resolution (Å)
Rmerge F obs
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. possible
Num. unique obs
Rrim(I) all
Diffraction-ID
% possible all
2.25-2.33
0.773
0.485
1.5
4349
3615
2641
0.661
1
73.1
2.33-2.42
0.836
0.432
1.9
6013
3609
3267
0.579
90.5
2.42-2.53
0.866
0.362
2.2
7068
3676
3639
0.486
99
2.53-2.67
0.917
0.279
2.8
7422
3869
3816
0.376
98.6
2.67-2.83
0.948
0.219
3.7
6795
3512
3477
0.295
99
2.83-3.05
0.976
0.143
5.4
7201
3734
3691
0.194
98.8
3.05-3.36
0.992
0.086
8.2
7185
3715
3681
0.116
99.1
3.36-3.84
0.996
0.057
11.9
6997
3638
3564
0.077
98
3.84-4.83
0.998
0.04
15.9
7103
3691
3616
0.054
98
4.83-29.328
0.998
0.037
16
7131
3748
3634
0.051
97
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
XDS
datareduction
XSCALE
November3, 2014BUILT=20141118
datascaling
SHELXD
phasing
BUSTER
2.10.2
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.25→29.328 Å / Cor.coef. Fo:Fc: 0.9509 / Cor.coef. Fo:Fc free: 0.9227 / Occupancy max: 1 / Occupancy min: 0.5 / 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. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. CL IONS MODELED WERE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
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