- PDB-4me8: Crystal structure of a signal peptidase I (EF3073) from Enterococ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4me8
Title
Crystal structure of a signal peptidase I (EF3073) from Enterococcus faecalis V583 at 2.27 A resolution
Components
Signal peptidase I
Keywords
HYDROLASE / PF00717 family / Peptidase_S24 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information
signal peptidase I / membrane => GO:0016020 / serine-type endopeptidase activity / plasma membrane Similarity search - Function
Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / Umud Fragment, subunit A ...Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA/Signal peptidase-like superfamily / Ribbon / Mainly Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 39 / 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 29-178 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: 1.73 Å3/Da / Density % sol: 28.92 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 20.00% polyethylene glycol 3350, 0.200M ammonium fluoride, No Buffer pH 6.2, Additive: 0.001 M leupeptin, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 26, 2011 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97944
1
3
0.97894
1
Reflection
Resolution: 2.27→28.174 Å / Num. obs: 6200 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.346 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.93
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
2.27-2.35
0.777
1.7
3675
1057
99.1
2.35-2.44
0.61
2.3
4016
998
100
2.44-2.56
0.535
2.5
4566
1156
99.7
2.56-2.69
0.378
3.7
4143
1046
99.8
2.69-2.86
0.215
5.9
4149
1069
99.6
2.86-3.08
0.132
8.8
3803
1056
99.2
3.08-3.39
0.091
13.9
4319
1070
99.9
3.39-3.87
0.054
21.6
4127
1043
99.9
3.87-4.87
0.037
27.8
3894
1065
98.6
4.87
0.033
30.8
4212
1094
98.3
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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
REFMAC
5.7.0032
refinement
XDS
datareduction
XSCALE
datascaling
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.27→28.174 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.192 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.359 / ESU R Free: 0.248 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN 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. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED. 7. ELECTRON DENSITY IS DISORDERED AROUND RAMACHANDRAN OUTLIER RESIDUE A109.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.258
486
7.9 %
RANDOM
Rwork
0.2124
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obs
0.2162
6146
99.53 %
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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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