- PDB-3ty1: Crystal structure of a putative aldose 1-epimerase (KPN_04629) fr... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3ty1
Title
Crystal structure of a putative aldose 1-epimerase (KPN_04629) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.90 A resolution
Components
Hypothetical aldose 1-epimerase
Keywords
ISOMERASE / Supersandwich / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Protein of unknown function DUF4432 / Domain of unknown function (DUF4432) / Beta-galactosidase; Chain A, domain 5 - #10 / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich / Mainly Beta / Putative thioredoxin-like protein
Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
THIS CONSTRUCT (RESIDUES 20-402) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 20-402) 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40.00% 2-methyl-2,4-pentanediol, 0.20M ammonium sulfate, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 1.9→29.698 Å / Num. all: 113332 / Num. obs: 113332 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.331 Å2 / Rsym value: 0.074 / Net I/σ(I): 9.8
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
1.9-1.95
3.8
0.561
2.3
31646
8363
0.561
100
1.95-2
3.8
0.435
2.8
31168
8198
0.435
100
2-2.06
3.8
0.352
3.4
30109
7909
0.352
100
2.06-2.12
3.8
0.3
4
29076
7648
0.3
100
2.12-2.19
3.8
0.235
4.8
28570
7479
0.235
100
2.19-2.27
3.8
0.196
5.8
27695
7272
0.196
100
2.27-2.36
3.8
0.166
6.3
26503
6920
0.166
100
2.36-2.45
3.8
0.141
7.2
25754
6726
0.141
100
2.45-2.56
3.8
0.125
8
24630
6414
0.125
100
2.56-2.69
3.8
0.111
9.6
23757
6192
0.111
100
2.69-2.83
3.8
0.104
10.9
22450
5838
0.104
100
2.83-3
3.8
0.091
13
21369
5558
0.091
100
3-3.21
3.8
0.074
15.7
20033
5211
0.074
100
3.21-3.47
3.8
0.063
18.3
18672
4854
0.063
100
3.47-3.8
3.8
0.052
20.6
17164
4462
0.052
100
3.8-4.25
3.8
0.044
22.4
15661
4069
0.044
100
4.25-4.91
3.8
0.044
24.1
13717
3570
0.044
100
4.91-6.01
3.8
0.048
23.5
11636
3032
0.048
100
6.01-8.5
3.8
0.046
22.6
9043
2367
0.046
100
8.5-29.698
3.7
0.038
24.9
4568
1250
0.038
95.2
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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
SCALA
3.3.15
datascaling
REFMAC
5.5.0110
refinement
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.9→29.698 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 6.177 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.114 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.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.2-METHYL-2,4-PENTANEDIOL (MPD) AND SULFATE (SO4) FROM THE CRYSTALLIZATION SOLUTION AND CHLORIDE (CL) FROM THE PURIFICATION BUFFER HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1931
5671
5 %
RANDOM
Rwork
0.1581
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obs
0.1598
113323
99.96 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
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