- PDB-4got: Crystal structure of a putative methionine-binding lipoprotein (B... -
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Open data
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Basic information
Entry
Database: PDB / ID: 4got
Title
Crystal structure of a putative methionine-binding lipoprotein (BSU32730) from Bacillus subtilis subsp. subtilis str. 168 at 1.95 A resolution
Components
Methionine-binding lipoprotein metQ
Keywords
LIPID BINDING PROTEIN / NLPA lipoprotein / PF03180 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / METHIONINE-BINDING PROTEIN
Mass: 18.015 Da / Num. of mol.: 175 / 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 RESIDUES 27-274 OF 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 40.0% polyethylene glycol 400, 0.2M lithium sulfate, 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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97879 Å / Relative weight: 1
Reflection
Resolution: 1.95→44.561 Å / Num. obs: 16953 / % possible obs: 89.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.42 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.54
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
1.95-2.02
0.588
2.2
3873
935
50.8
2.02-2.1
0.496
2.9
6211
1303
69.8
2.1-2.2
0.38
4.1
9148
1676
86.2
2.2-2.31
0.31
6
11572
1756
99.1
2.31-2.46
0.232
7.4
12964
1922
99.1
2.46-2.65
0.179
9.1
12083
1859
98.6
2.65-2.91
0.138
11.9
12255
1813
99.4
2.91-3.33
0.09
16.2
12126
1867
98.2
3.33-4.19
0.063
22
11996
1870
98.2
4.19
0.061
24.6
12425
1952
98.3
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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
5.6.0117
refinement
XDS
datareduction
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.95→44.561 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.997 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.172 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. A SULFATE ION (SO4) FROM THE CRYSTALLIZATION SOLUTION IS MODELED. 7. A SELENOMETHIONINE RESIDUE IS MODELED IN THE ACTIVE SITE BASED ON ELECTRON DENSITY AND ANOMALOUS DIFFERENCE FOURIER MAP. 8. RAMACHANDRAN OUTLIER PHE 85 IS SUPPORTED BY ELECTRON DENSITY AND IS LIKELY A DISTORTION CAUSED BY LIGAND BINDING.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2286
876
5.2 %
RANDOM
Rwork
0.1717
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obs
0.1747
16950
90.24 %
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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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