- PDB-4pw1: Crystal structure of a protein with unknown function (CLOLEP_0246... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4pw1
Title
Crystal structure of a protein with unknown function (CLOLEP_02462) from Clostridium leptum DSM 753 at 2.10 A resolution
Components
Uncharacterized protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / an orphan protein / unique fold: a nine stranded anti-parallel beta sheet surrounded by alpha-helices / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Uncharacterized protein
Function and homology information
Biological species
Clostridium leptum (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT (RESIDUES 35-285) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 35-285) 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: 2.33 Å3/Da / Density % sol: 47.14 %
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal 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
0.97959
1
3
0.97903
1
Reflection
Resolution: 2.1→29.907 Å / Num. all: 33887 / Num. obs: 33887 / % possible obs: 99.6 % / Redundancy: 5.9 % / Rsym value: 0.077 / Net I/σ(I): 14.5
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
2.1-2.15
5.4
0.285
2.7
13137
2425
0.285
99.1
2.15-2.21
5.6
0.255
3
13371
2370
0.255
98.8
2.21-2.28
6.3
0.235
3.3
14773
2329
0.235
99.9
2.28-2.35
6.3
0.206
3.8
14316
2272
0.206
99.9
2.35-2.42
6.1
0.183
4.2
13595
2223
0.183
100
2.42-2.51
5.9
0.16
4.8
12509
2119
0.16
100
2.51-2.6
5.6
0.133
5.7
11534
2075
0.133
99.9
2.6-2.71
5.4
0.114
6.7
10588
1948
0.114
98.5
2.71-2.83
6.2
0.108
6.9
12048
1930
0.108
100
2.83-2.97
6.3
0.092
7.9
11385
1818
0.092
100
2.97-3.13
6.1
0.078
8.8
10786
1779
0.078
100
3.13-3.32
6
0.068
9.6
9890
1659
0.068
100
3.32-3.55
5.3
0.057
11.3
8205
1552
0.057
99
3.55-3.83
6.4
0.053
11.4
9587
1488
0.053
100
3.83-4.2
6.1
0.05
12.2
8311
1353
0.05
99.9
4.2-4.7
5.9
0.048
12.1
7354
1255
0.048
100
4.7-5.42
5.2
0.051
11.7
5713
1100
0.051
99.1
5.42-6.64
6
0.057
11
5822
971
0.057
100
6.64-9.39
5.4
0.05
10.8
4142
771
0.05
99.8
9.39-29.907
5.1
0.046
10.5
2293
450
0.046
94.7
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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
SCALA
3.3.20
datascaling
REFMAC
5.7.0029
refinement
MOSFLM
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.1→29.907 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 6.664 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.146 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 SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. GLYCEROL (GOL) USED AS A CRYOPROTECTANT HAS BEEN MODELED INTO THE STRUCTURE
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.197
1715
5.1 %
RANDOM
Rwork
0.1636
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obs
0.1653
33813
99.37 %
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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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