- PDB-4nrd: Crystal structure of a putative GDSL-like lipase (BACOVA_04955) f... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4nrd
Title
Crystal structure of a putative GDSL-like lipase (BACOVA_04955) from Bacteroides ovatus ATCC 8483 at 2.10 A resolution
Components
Uncharacterized protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Lipase_GDSL_lke protein / PF16255 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
A: Uncharacterized protein B: Uncharacterized protein C: Uncharacterized protein D: Uncharacterized protein E: Uncharacterized protein F: Uncharacterized protein hetero molecules
Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY RESIDUES 21-228 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: 2.06 Å3/Da / Density % sol: 40.29 %
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013 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: 0.97937 Å / Relative weight: 1
Reflection
Resolution: 2.1→29.391 Å / Num. all: 61839 / Num. obs: 61839 / % possible obs: 82.2 % / Redundancy: 2.3 % / Rsym value: 0.102 / Net I/σ(I): 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
2.1-2.15
2.3
0.463
1.9
10781
4744
0.463
84.3
2.15-2.21
2.3
0.365
2.2
10179
4433
0.365
82.3
2.21-2.28
2.3
0.336
2.4
9093
4010
0.336
76.1
2.28-2.35
2.2
0.296
2.6
8654
3866
0.296
75.4
2.35-2.42
2.3
0.277
2.8
9829
4268
0.277
86.3
2.42-2.51
2.3
0.229
3.3
9609
4162
0.229
86.4
2.51-2.6
2.3
0.187
3.7
8770
3864
0.187
83.7
2.6-2.71
2.3
0.172
4.2
8332
3654
0.172
81.3
2.71-2.83
2.3
0.143
5
6912
3057
0.143
71.8
2.83-2.97
2.3
0.117
5.9
7989
3491
0.117
85.2
2.97-3.13
2.3
0.093
7.1
7733
3331
0.093
86.1
3.13-3.32
2.3
0.084
8.1
7293
3180
0.084
86
3.32-3.55
2.3
0.071
9.5
6522
2862
0.071
82.5
3.55-3.83
2.2
0.059
11.8
5428
2415
0.059
76
3.83-4.2
2.3
0.058
13
6199
2668
0.058
89.7
4.2-4.7
2.3
0.058
13.4
5361
2320
0.058
86.7
4.7-5.42
2.2
0.055
13
4003
1788
0.055
75.8
5.42-6.64
2.3
0.063
11.9
3961
1720
0.063
87.4
6.64-9.39
2.3
0.058
12.9
3041
1316
0.058
84.9
9.39-29.391
2.3
0.064
15.4
1584
690
0.064
82.3
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Phasing
Phasing
Method: molecular replacement
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
PHASER
2.3.0
phasing
SCALA
3.3.20
datascaling
BUSTER-TNT
2.10.0
refinement
MOSFLM
datareduction
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.391 Å / Cor.coef. Fo:Fc: 0.9478 / Cor.coef. Fo:Fc free: 0.9277 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM ...Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 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. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT USING LSSR (-AUTONCS) IN BUSTER. 7. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED.
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