- PDB-4h3w: Crystal structure of a putative secreted protein (BDI_1231) from ... -
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Basic information
Entry
Database: PDB / ID: 4h3w
Title
Crystal structure of a putative secreted protein (BDI_1231) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution
Components
hypothetical protein
Keywords
Structural Genomics / Unknown Function / two beta barrel domains / secreted protein / ORFan / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Jelly Rolls - #1260 / Protein of unknown function (DUF4621), C-terminal domain / Protein of unknown function DUF4621 / Protein of unknown function (DUF4621) / Hypothetical Protein Tm1070; Chain: A / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological species
Parabacteroides distasonis (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Sequence details
1. THE CONSTRUCT (RESIDUES 24-352) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...1. THE CONSTRUCT (RESIDUES 24-352) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.
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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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30.0% polyethylene glycol 4000, 0.2M magnesium chloride, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2012 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97885 Å / Relative weight: 1
Reflection
Resolution: 1.87→48.317 Å / Num. obs: 53817 / % possible obs: 87.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.595 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.4
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
1.87-1.94
0.57
1.8
13764
3971
61.5
1.94-2.01
0.421
2.5
18617
5095
91.8
2.01-2.11
0.271
3.9
22778
6262
93
2.11-2.22
0.215
4.8
20391
5569
92
2.22-2.36
0.155
6.8
20208
5563
90.1
2.36-2.54
0.116
9.1
21096
5706
93.5
2.54-2.79
0.088
12.2
19498
5339
88.1
2.79-3.19
0.057
18.5
20446
5572
90.5
3.19-4.02
0.04
24.5
19209
5284
85.3
4.02
0.038
28.4
19668
5456
87.7
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Phasing
Phasing
Method: SAD
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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
REFMAC
5.7.0029
refinement
XDS
datareduction
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.87→48.317 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.939 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.155 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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.SOLVENT WAS EXCLUDED FROM TLS REFINEMENT. 4. THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY).5. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 6. THE NOMINAL RESOLUTION IS 2.00 ANGSTROMS WITH 7826 OBSERVED REFLECTIONS BETWEEN 2.00-1.87 (71.2% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2382
2703
5.1 %
RANDOM
Rwork
0.1963
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obs
0.1984
53272
86.62 %
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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: BABINET MODEL WITH MASK
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