- PDB-3ec4: Crystal structure of Putative Acetyltransferase from the GNAT fam... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3ec4
Title
Crystal structure of Putative Acetyltransferase from the GNAT family (YP_497011.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.80 A resolution
Components
Putative Acetyltransferase from the GNAT family
Keywords
TRANSFERASE / YP_497011.1 / Putative Acetyltransferase from the GNAT family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Acetyltransferase (GNAT) family
Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O
Sequence details
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT 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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.43 Details: 33.8% polyethylene glycol 4000, 0.2M sodium acetate, 0.1M TRIS pH 8.43, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97837
1
Reflection
Resolution: 1.8→29.21 Å / Num. obs: 38799 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.581 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 5.628
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.8-1.85
3.7
0.505
1.5
10441
2849
0.505
100
1.85-1.9
3.7
0.433
1.8
10154
2746
0.433
99.7
1.9-1.95
3.7
0.343
2.2
9807
2664
0.343
99.7
1.95-2.01
3.7
0.276
2.8
9588
2603
0.276
99.9
2.01-2.08
3.7
0.233
3.3
9267
2509
0.233
99.7
2.08-2.15
3.7
0.204
3.7
8983
2449
0.204
99.9
2.15-2.23
3.7
0.178
4.2
8724
2373
0.178
99.8
2.23-2.32
3.7
0.163
4.5
8316
2252
0.163
99.9
2.32-2.43
3.7
0.146
5
8062
2201
0.146
100
2.43-2.55
3.7
0.132
5.4
7739
2102
0.132
100
2.55-2.68
3.7
0.113
6.3
7339
2009
0.113
99.9
2.68-2.85
3.7
0.099
7.1
6930
1893
0.099
99.9
2.85-3.04
3.6
0.088
7.7
6559
1808
0.088
100
3.04-3.29
3.6
0.075
8.7
6027
1660
0.075
100
3.29-3.6
3.6
0.065
9.9
5625
1557
0.065
100
3.6-4.02
3.5
0.061
10
5082
1433
0.061
100
4.02-4.65
3.6
0.057
10.9
4466
1247
0.057
99.9
4.65-5.69
3.5
0.064
9.2
3791
1085
0.064
99.9
5.69-8.05
3.4
0.072
7.8
2896
858
0.072
99.8
8.05-29.21
3.1
0.064
8.7
1539
501
0.064
97.2
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.8→29.21 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.232 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.128 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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. ACETATE FROM THE CRYSTALLIZATION BUFFER IS MODELED INTO THE STRUCTURE. 4. ELECTRON DENSITY CORRESPONDING TO GLY 121 ON THE B-SUBUNIT IS DISORDERED; THEREFORE, THIS RESIDUE WAS NOT MODELED. 5. ELECTRON DENSITIES FOR GLY 0 MSE 1, SER 2, AND GLU 3 AT THE N-TERMINUS OF BOTH SUBUNITS IN THE ASYMMETRIC UNIT ARE DISORDERED; THERFORE THESE RESIDUES WERE NOT MODELED. 6.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.215
1941
5 %
RANDOM
Rwork
0.171
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-
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obs
0.173
38743
99.78 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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