- PDB-3ele: Crystal structure of Amino Transferase (RER070207001803) from Eub... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3ele
Title
Crystal structure of Amino Transferase (RER070207001803) from Eubacterium rectale at 2.10 A resolution
Components
Amino Transferase
Keywords
TRANSFERASE / RER070207001803 / Amino Transferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Aminotransferase class I and II
Function / homology
Function and homology information
Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / pyridoxal phosphate binding Similarity search - Function
Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.0000M LiCl, 20.0000% PEG-6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 2.1→29.881 Å / Num. obs: 92103 / % possible obs: 97.6 % / Redundancy: 2 % / Biso Wilson estimate: 25.239 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 9.121
Reflection shell
Diffraction-ID: 1 / Redundancy: 2 %
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.1-2.15
0.35
2.1
13457
6769
0.35
96.7
2.15-2.21
0.299
2.2
13057
6562
0.299
96.8
2.21-2.28
0.259
1.7
12848
6459
0.259
97.1
2.28-2.35
0.209
3.5
12474
6265
0.209
97
2.35-2.42
0.19
3.9
12017
6040
0.19
97.2
2.42-2.51
0.17
4.4
11655
5853
0.17
97.3
2.51-2.6
0.147
5.1
11250
5647
0.147
97.4
2.6-2.71
0.126
5.7
10851
5452
0.126
97.5
2.71-2.83
0.106
7
10486
5268
0.106
97.7
2.83-2.97
0.086
8.4
9973
5010
0.086
97.8
2.97-3.13
0.068
10.5
9496
4769
0.068
97.9
3.13-3.32
0.052
13.7
8991
4515
0.052
98.1
3.32-3.55
0.045
15.1
8446
4242
0.045
98
3.55-3.83
0.037
17.9
7930
3988
0.037
98.3
3.83-4.2
0.034
18.1
7236
3637
0.034
98.5
4.2-4.7
0.031
21
6620
3324
0.031
98.5
4.7-5.42
0.035
17.5
5811
2920
0.035
98.7
5.42-6.64
0.039
16.5
4908
2467
0.039
98.7
6.64-9.39
0.037
15.8
3797
1907
0.037
98.8
9.39-29.89
0.037
15.8
1996
1009
0.037
95.7
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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
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.1→29.881 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 10.333 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 MOLECULES FROM THE CRYO SOLUTION ARE MODELED. 5. LIGAND MOLECULE PLP IS MODELED ON THE BASIS OF DENSITY AND HOMOLOGOUS STRUCTURES 1O4S, 1XI9. 6. RAMACHANDRAN OUTLIER RESIDUES 217 ARE WELL SUPPORTED BY DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.222
4610
5 %
RANDOM
Rwork
0.173
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-
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obs
0.175
92101
97.57 %
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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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