- PDB-3tdq: Crystal structure of a fimbrial biogenesis protein PilY2 (PilY2_P... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3tdq
Title
Crystal structure of a fimbrial biogenesis protein PilY2 (PilY2_PA4555) from Pseudomonas aeruginosa PAO1 at 2.10 A resolution
Components
PilY2 protein
Keywords
CELL ADHESION / fimbiria / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Type 4 fimbrial biogenesis protein PilY2 / Type 4 fimbrial biogenesis protein PilY2 / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF superfamily / type IV pilus-dependent motility / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / PilY2 protein
Function and homology information
Biological species
Pseudomonas aeruginosa (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (RESIDUES 19-115) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 19-115) 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: 2.33 Å3/Da / Density % sol: 47.15 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND .
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 15.00% Glycerol, 0.17M NH4OAc, 25.50% PEG-4000, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2011 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
Radiation
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
0.97901
1
2
0.91162
1
3
0.97876
1
Reflection
Resolution: 2.1→25.556 Å / Num. obs: 12753 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.782 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.94
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.1-2.17
0.33
2.4
3708
1968
1
86.7
2.17-2.26
0.299
2.8
4710
2447
1
99.1
2.26-2.36
0.232
3.6
4491
2346
1
99.4
2.36-2.49
0.196
4.4
4772
2480
1
99.2
2.49-2.64
0.147
5.6
4441
2299
1
99.1
2.64-2.85
0.115
7.2
4747
2458
1
99
2.85-3.13
0.064
11.7
4503
2332
1
99.3
3.13-3.59
0.04
17.3
4624
2392
1
98.4
3.59-4.51
0.024
25.5
4526
2329
1
97.6
4.51-25.556
0.024
28.4
4565
2329
1
95.5
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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
December6, 2010
datascaling
BUSTER-TNT
2.8.0
refinement
XDS
datareduction
SHELXD
phasing
BUSTER
2.8.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.1→25.556 Å / Cor.coef. Fo:Fc: 0.9463 / Cor.coef. Fo:Fc free: 0.9366 / 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. CHLORIDE, SODIUM, GLYCEROL AND ACETATE MODELED ARE PRESENT IN CRYSTALLIZATION/PROTEIN BUFFER CONDITIONS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
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