- PDB-3ege: Crystal structure of Putative methyltransferase from antibiotic b... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3ege
Title
Crystal structure of Putative methyltransferase from antibiotic biosynthesis pathway (YP_324569.1) from ANABAENA VARIABILIS ATCC 29413 at 2.40 A resolution
Components
Putative methyltransferase from antibiotic biosynthesis pathway
Keywords
TRANSFERASE / YP_324569.1 / Putative methyltransferase from antibiotic biosynthesis pathway / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Methyltransferase domain
Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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: 3.82 Å3/Da / Density % sol: 67.81 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 31.0% ethylene glycol, 0.1M phosphate-citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97915 Å / Relative weight: 1
Reflection
Resolution: 2.4→29.761 Å / Num. obs: 18494 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 48.467 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 6.022
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
2.4-2.46
5.6
0.714
1.1
7507
1335
0.714
98.7
2.46-2.53
6.8
0.647
1.1
8624
1266
0.647
99.9
2.53-2.6
8.6
0.565
1.4
11109
1287
0.565
100
2.6-2.68
9.2
0.487
1.6
11458
1240
0.487
100
2.68-2.77
9.3
0.389
2
11144
1203
0.389
100
2.77-2.87
9.3
0.333
2.3
10936
1179
0.333
100
2.87-2.98
9.3
0.259
2.9
10395
1120
0.259
100
2.98-3.1
9.2
0.187
4
10127
1095
0.187
100
3.1-3.24
9.2
0.157
4.6
9635
1043
0.157
100
3.24-3.39
9.2
0.122
6
9095
988
0.122
100
3.39-3.58
9.2
0.095
7.6
8849
967
0.095
100
3.58-3.79
9.2
0.077
9
8436
919
0.077
100
3.79-4.06
9.1
0.066
10.2
7760
854
0.066
100
4.06-4.38
9
0.064
10.1
7111
786
0.064
100
4.38-4.8
9
0.064
9.8
6728
750
0.064
100
4.8-5.37
8.9
0.068
9.5
6023
680
0.068
100
5.37-6.2
8.8
0.069
9.4
5279
602
0.069
100
6.2-7.59
8.6
0.076
8.3
4525
525
0.076
100
7.59-10.73
8.3
0.045
13
3449
414
0.045
100
10.73-29.76
7.4
0.044
12
1788
241
0.044
95.2
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Phasing
Phasing
Method: SAD
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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: SAD / Resolution: 2.4→29.761 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.455 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.172 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 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. EDO MOLECULE FROM THE CRYSTALLIZATION SOLUTION IS MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.202
946
5.1 %
RANDOM
Rwork
0.182
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obs
0.184
18460
99.76 %
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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: BABINET MODEL WITH MASK
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