- PDB-4mxt: Crystal structure of an Outer-membrane lipoprotein carrier protei... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4mxt
Title
Crystal structure of an Outer-membrane lipoprotein carrier protein (BACUNI_04723) from Bacteroides uniformis ATCC 8492 at 1.40 A resolution
Components
Uncharacterized protein
Keywords
PROTEIN TRANSPORT / LolA-like prokaryotic lipoproteins and lipoprotein localization factors fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Outer membrane lipoprotein carrier protein LolA / Lipoprotein localisation LolA/LolB/LppX / Outer membrane lipoprotein carrier protein LolA-like / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / Mainly Beta / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological species
Bacteroides uniformis (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT (RESIDUES 28-216) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 28-216) 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.20M di-ammonium tartrate, 20.)% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97971
1
3
0.97894
1
Reflection
Resolution: 1.4→27.049 Å / Num. obs: 36767 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.93 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 10.3
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
1.4-1.45
0.38
1.7
8448
5956
79.7
1.45-1.51
0.275
2.2
9541
6863
88.1
1.51-1.58
0.17
3.5
10200
7014
92.9
1.58-1.66
0.128
4.6
9442
6568
92.4
1.66-1.76
0.093
6.1
9106
6481
89
1.76-1.9
0.064
8.8
10246
7135
93.2
1.9-2.09
0.044
13.3
9998
6935
92.8
2.09-2.39
0.036
16.8
9513
6685
89.4
2.39-3.01
0.03
19.9
9986
6883
91.9
3.01
0.021
25.3
9705
6655
88.3
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
PHENIX
1.8.2
refinement
XDS
datareduction
XSCALE
datascaling
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.4→27.049 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 0.13 / σ(F): 1.9 / Phase error: 16.44 / Stereochemistry target values: MLHL 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.POLYETHYLENE GLYCOL FRAGMENTS (PEG) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Rfree
0.1733
1850
5.03 %
Rwork
0.1428
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obs
0.1443
36766
96.15 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
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