- PDB-3pnx: Crystal structure of a putative sulfurtransferase dsrE (Swol_2425... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3pnx
Title
Crystal structure of a putative sulfurtransferase dsrE (Swol_2425) from Syntrophomonas wolfei str. Goettingen at 1.92 A resolution
Components
Putative sulfurtransferase dsrE
Keywords
TRANSFERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
DsrE2-like family / DsrE/DsrF/DrsH-like family / DsrEFH-like / DsrEFH-like / Hypothetical Protein Ychn; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological species
Syntrophomonas wolfei (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNEMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
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Components
#1: Protein
PutativesulfurtransferasedsrE
Mass: 18700.412 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Syntrophomonas wolfei (bacteria) / Strain: Goettingen / Gene: Swol_2425 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q0AU90
Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Monochromator: DOUBLE CRYSTAL SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.9796
1
3
0.97925
1
Reflection
Resolution: 1.92→29.453 Å / Num. obs: 72995 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.721 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 15.37
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.92-1.99
0.566
1.4
27192
13916
1
94.7
1.99-2.07
0.387
2.1
27483
13916
1
95.9
2.07-2.16
0.263
3.1
26444
13404
1
96.5
2.16-2.28
0.166
4.9
29013
14699
1
96.3
2.28-2.42
0.115
6.9
26982
13678
1
96.6
2.42-2.6
0.071
10.9
26676
13535
1
96.6
2.6-2.87
0.049
15.2
28662
14540
1
96.5
2.87-3.28
0.028
24.2
26615
13535
1
95.1
3.28-4.13
0.017
38.3
26944
13727
1
94.6
4.13-29.453
0.014
47.5
26866
13769
1
94.4
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
SHELX
phasing
REFMAC
5.5.0110
refinement
XSCALE
datascaling
PDB_EXTRACT
3.1
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.92→29.453 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.787 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.142 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. SODIUM (NA) AND CHLORIDE (CL) IONS HAVE BEEN MODELED INTO THE STRUCTURE. 4. ELECTRON DENSITY SUPPORTS THE MODELING OF CYS 120 ON THE SIX SUBUNITS IN THE ASYMMETRIC UNIT AS CYSTEINESULFONIC ACID (OCS). 5. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 5. LEU 83 ON THE C AND E SUBUNITS AND ASN 82 ON THE E SUBUNIT ARE IN REGIONS WHERE ELECTRON DENSITIES ARE DISORDERED, AND THESE RESIDUES ARE RAMACHANDRAN OUTLIERS IN MOLPROBITY. 6. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 7. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2152
3687
5.1 %
RANDOM
Rwork
0.1896
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-
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obs
0.1909
72993
98.78 %
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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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