THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN FORMING A DIMER. CRYSTAL PACKING ANALYSIS SUGGESTS THAT A DIMER IS THE STABLE OLIGOMERIC FORM IN SOLUTION.
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Components
#1: Protein
LD-carboxypeptidaseA / Peptidase U61
Mass: 29685.783 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria) Strain: DSM 12444 / Gene: Saro_1426, YP_496704.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2G8F3
Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: NANODROP, 1.60M (NH4)2SO4, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.89→29.709 Å / Num. obs: 47086 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 5.451
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
1.89-1.95
3.6
0.845
0.9
12254
3423
0.845
100
1.95-2
4.4
0.627
1.2
14723
3355
0.627
100
2-2.06
4.4
0.533
1.4
14168
3231
0.533
100
2.06-2.12
4.4
0.441
1.7
13954
3174
0.441
100
2.12-2.19
4.4
0.356
2.2
13713
3107
0.356
100
2.19-2.27
4.4
0.312
2.5
12849
2938
0.312
100
2.27-2.36
4.4
0.283
2.7
12617
2888
0.283
100
2.36-2.45
4.4
0.254
3
12179
2755
0.254
100
2.45-2.56
4.4
0.21
3.7
11678
2665
0.21
100
2.56-2.69
4.4
0.185
4.1
11173
2564
0.185
100
2.69-2.83
4.4
0.16
4.8
10617
2425
0.16
100
2.83-3
4.4
0.133
5.6
10042
2303
0.133
100
3-3.21
4.4
0.098
7.3
9499
2182
0.098
100
3.21-3.47
4.3
0.08
8.8
8845
2038
0.08
100
3.47-3.8
4.3
0.061
11.2
8109
1877
0.061
100
3.8-4.25
4.3
0.053
12.5
7378
1714
0.053
99.9
4.25-4.91
4.3
0.051
12.3
6556
1529
0.051
99.8
4.91-6.01
4.2
0.059
11
5450
1294
0.059
99.7
6.01-8.5
4.2
0.054
12.2
4305
1036
0.054
99.4
8.5-29.709
3.8
0.042
14.8
2237
588
0.042
96.3
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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
MAR345
CCD
datacollection
MOSFLM
datareduction
autoSHARP
phasing
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.89→29.709 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 6.525 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.129 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. SULFATE (SO4) FROM THE CRYSTALLIZATION AND GLYCEROL (GOL) FROM THE CRYOPROTECTANT CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED IN THE INTERFACE OF THE DIMER IN THE CRYSTAL STRUCTURE. THIS IS NOT THE PUTATIVE ACTIVE SITE OF THE PROTEIN.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.207
2381
5.1 %
RANDOM
Rwork
0.171
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-
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obs
0.173
47036
99.47 %
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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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