- PDB-3d33: Crystal structure of a duf3244 family protein with an immunoglobu... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3d33
Title
Crystal structure of a duf3244 family protein with an immunoglobulin-like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc 8482 at 1.70 A resolution
Components
Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold
Keywords
UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Immunoglobulin-like - #3080 / Protein of unknown function DUF3244 / Domain of unknown function (DUF3244) / Immunoglobulin-like / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological species
Bacteroides vulgatus ATCC 8482 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
A: Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold B: Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold
AUTHORS STATE THAT ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY (anSEC) SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Mass: 18.015 Da / Num. of mol.: 283 / 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. THE CLONED CONSTRUCT CONTAINS RESIDUES 28-134 OF THE FULL LENGTH PROTEIN. THIS REMOVED THE PUTATIVE SIGNAL PEPTIDE WHOSE PREDICTED CLEAVAGE SITE IS BETWEEN RESIDUES 28-29.
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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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 0.2000M MgFormate, 20.0000% PEG-3350, No Buffer pH 5.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Relative weight: 1
Reflection
Resolution: 1.7→28.677 Å / Num. obs: 25116 / % possible obs: 99.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 24.306 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 4.6
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
1.7-1.74
7
0.871
0.9
12323
1763
0.871
95.7
1.74-1.79
7.4
0.696
1.1
13415
1803
0.696
100
1.79-1.84
7.4
0.55
1.4
13163
1769
0.55
100
1.84-1.9
7.5
0.432
1.8
12677
1698
0.432
100
1.9-1.96
7.4
0.335
2.2
12476
1675
0.335
100
1.96-2.03
7.4
0.25
2.9
11840
1594
0.25
100
2.03-2.11
7.4
0.203
3.6
11366
1530
0.203
100
2.11-2.19
7.4
0.177
4.1
11136
1495
0.177
100
2.19-2.29
7.4
0.157
4.5
10606
1425
0.157
100
2.29-2.4
7.4
0.139
5
10194
1370
0.139
100
2.4-2.53
7.5
0.123
5.5
9715
1303
0.123
100
2.53-2.69
7.4
0.105
6.3
9233
1240
0.105
100
2.69-2.87
7.5
0.095
6.6
8635
1156
0.095
100
2.87-3.1
7.5
0.084
7.6
8099
1083
0.084
100
3.1-3.4
7.5
0.073
8.3
7440
996
0.073
100
3.4-3.8
7.5
0.067
8.7
6694
896
0.067
100
3.8-4.39
7.4
0.066
8.8
6017
809
0.066
100
4.39-5.38
7.3
0.068
8.6
5004
681
0.068
100
5.38-7.6
7.1
0.072
8.7
3807
534
0.072
100
7.6-28.68
6.7
0.063
9.4
1979
296
0.063
97.2
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3.004
dataextraction
MOSFLM
datareduction
Refinement
Method to determine structure: SAD / Resolution: 1.7→28.677 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.951 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.104 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 RESIDUAL B FACTORS ONLY. 4. THE FOLLOWING REGIONS ARE DISORDERED: A/B0, A/B28-33, A47-53, B46-53.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22
1283
5.1 %
RANDOM
Rwork
0.174
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obs
0.176
25099
99.63 %
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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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