- PDB-4lda: Crystal structure of a CheY-like protein (tadZ) from Pseudomonas ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4lda
Title
Crystal structure of a CheY-like protein (tadZ) from Pseudomonas aeruginosa PAO1 at 2.70 A resolution
Components
TadZ
Keywords
TRANSCRIPTION / Response regulator receiver domain / PF00072 / CheY-like fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information
negative regulation of cell division / cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (1-130) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (1-130) 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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.010M nickel (II) chloride, 0.70M lithium sulfate, 0.1M TRIS pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 2.4→47.962 Å / Num. obs: 59828 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 70.075 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.57
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.4-2.46
2.95
2.108
0.61
13124
4455
99.8
2.46-2.53
1.608
0.8
12719
4298
99.8
2.53-2.6
1.096
1.2
12540
4247
99.8
2.6-2.68
0.964
1.4
11757
4037
98.8
2.68-2.77
0.715
1.8
11833
4004
99.9
2.77-2.87
0.477
2.6
11352
3828
99.8
2.87-2.98
0.339
3.5
10967
3711
99.8
2.98-3.1
0.23
5.1
10606
3593
99.8
3.1-3.24
0.155
7.1
9976
3404
99.5
3.24-3.39
0.101
10
9508
3263
99.5
3.39-3.58
0.074
13.5
8714
3065
97.6
3.58-3.79
0.059
16
8234
2897
97.8
3.79-4.06
0.048
18.8
7570
2703
96.7
4.06-4.38
0.038
21.9
7129
2536
98
4.38-4.8
0.032
24.2
6442
2311
96.3
4.8-5.37
0.035
24.9
5887
2103
96
5.37-6.2
0.036
24.4
5202
1868
96.8
6.2-7.59
0.033
25.5
4463
1592
97.7
7.59-10.73
0.022
32.1
3557
1228
96
10.73-47.96
0.022
32.6
1937
685
94.1
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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: 2.4→47.962 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.9361 / Occupancy max: 1 / Occupancy min: 0.37 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. SO4 ARE PRESENT IN CRYSTALLIZATION CONDITIONS. 5. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 6. THE DATA ARE ANISOTROPIC WITH A NOMINAL RESOLUTION OF 2.7 A. THERE WERE AN ADDITIONAL 15794 REFLECTIONS BETWEEN 2.4 - 2.7 A INCLUDED IN THE REFINEMENT, OF WHICH 3401 REFLECTIONS (18.8% OF THE POSSIBLE REFLECTIONS IN THE SHELL) HAD I/SIGI > 2.
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