- PDB-4hsp: Crystal structure of a DUF3299 family protein (PA4066) from Pseud... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4hsp
Title
Crystal structure of a DUF3299 family protein (PA4066) from Pseudomonas aeruginosa PAO1 at 2.45 A resolution
Components
hypothetical protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF11736 family protein / DUF3299 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / STRUCTURAL GENOMICS UNKNOWN FUNCTION
Function / homology
Protein of unknown function (DUF3299) / Protein of unknown function DUF3299 / Protein of unknown function (DUF3299) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Uncharacterized protein
Function and homology information
Biological species
Pseudomonas aeruginosa (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-172 OF 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: 3.9 Å3/Da / Density % sol: 68.48 %
Resolution: 2.45→29.234 Å / Num. obs: 9810 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 69.284 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.37
Reflection shell
Rmerge(I) obs: 0.014 / Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.45-2.54
1.6
11402
1784
96.3
2.54-2.64
1.9
13330
1727
99
2.64-2.76
3.8
13827
1776
99.8
2.76-2.9
5.4
13421
1727
99.9
2.9-3.08
9.2
13763
1768
100
3.08-3.32
14.8
14086
1811
100
3.32-3.65
21.4
13806
1774
100
3.65-4.18
31.8
14093
1818
100
4.18-5.25
39
13664
1779
100
5.25
43.1
13932
1826
99.2
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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
XSCALE
March15, 2012
datascaling
BUSTER-TNT
2.10.0
refinement
XDS
datareduction
SHELXD
phasing
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.45→29.234 Å / Cor.coef. Fo:Fc: 0.9609 / Cor.coef. Fo:Fc free: 0.9378 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. 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 4. EXPERIMENTAL (MAD) PHASE RESTRAINTS WERE USED DURING REFINEMENT. 5. SULFATE (SO4) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTION ARE MODELED.
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