- PDB-3lv4: Crystal structure of the glycoside hydrolase, family 43 YxiA prot... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3lv4
Title
Crystal structure of the glycoside hydrolase, family 43 YxiA protein from Bacillus licheniformis. Northeast Structural Genomics Consortium Target BiR14.
Components
Glycoside hydrolase YxiA
Keywords
HYDROLASE / Glycoside hydrolase / similar to arabinan endo-1 / 5-alpha-L-arabinosidase / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information
hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function
Resolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.2 / Num. unique all: 19695 / % possible all: 92.1
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Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SHELXDE
phasing
PHENIX
modelbuilding
PHENIX
(phenix.refine: 1.5_2)
refinement
DENZO
datareduction
SCALEPACK
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.695→45.244 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.38 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1903
9525
4.97 %
RANDOM
Rwork
0.1464
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-
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obs
0.1486
191496
96.74 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.318 Å2 / ksol: 0.405 e/Å3
Refinement step
Cycle: LAST / Resolution: 1.695→45.244 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6929
0
25
679
7633
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.006
7136
X-RAY DIFFRACTION
f_angle_d
1.056
9647
X-RAY DIFFRACTION
f_dihedral_angle_d
18.144
2534
X-RAY DIFFRACTION
f_chiral_restr
0.077
974
X-RAY DIFFRACTION
f_plane_restr
0.004
1266
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.6953-1.7145
0.282
252
0.1905
5081
X-RAY DIFFRACTION
81
1.7145-1.7347
0.2513
310
0.1851
5834
X-RAY DIFFRACTION
92
1.7347-1.7559
0.2761
267
0.1838
5984
X-RAY DIFFRACTION
95
1.7559-1.7781
0.2249
280
0.1664
5958
X-RAY DIFFRACTION
95
1.7781-1.8015
0.2304
289
0.1573
5986
X-RAY DIFFRACTION
96
1.8015-1.8262
0.2108
341
0.1611
6043
X-RAY DIFFRACTION
95
1.8262-1.8523
0.2447
286
0.1513
5937
X-RAY DIFFRACTION
96
1.8523-1.8799
0.2178
288
0.1493
6129
X-RAY DIFFRACTION
96
1.8799-1.9093
0.1935
302
0.145
5944
X-RAY DIFFRACTION
97
1.9093-1.9406
0.2323
280
0.1358
6059
X-RAY DIFFRACTION
96
1.9406-1.974
0.1945
344
0.1328
6029
X-RAY DIFFRACTION
96
1.974-2.0099
0.1953
307
0.1283
6057
X-RAY DIFFRACTION
96
2.0099-2.0486
0.1779
325
0.1182
6006
X-RAY DIFFRACTION
97
2.0486-2.0904
0.1935
357
0.1181
6074
X-RAY DIFFRACTION
97
2.0904-2.1359
0.1634
279
0.1251
6147
X-RAY DIFFRACTION
97
2.1359-2.1856
0.197
312
0.1307
6038
X-RAY DIFFRACTION
98
2.1856-2.2402
0.1856
363
0.1237
6199
X-RAY DIFFRACTION
98
2.2402-2.3008
0.1742
302
0.1152
6150
X-RAY DIFFRACTION
99
2.3008-2.3685
0.1625
376
0.1275
6113
X-RAY DIFFRACTION
99
2.3685-2.4449
0.1947
342
0.1323
6244
X-RAY DIFFRACTION
99
2.4449-2.5323
0.1979
356
0.1291
6229
X-RAY DIFFRACTION
99
2.5323-2.6337
0.1942
325
0.1379
6273
X-RAY DIFFRACTION
100
2.6337-2.7535
0.2114
321
0.1444
6189
X-RAY DIFFRACTION
100
2.7535-2.8987
0.1774
358
0.1401
6222
X-RAY DIFFRACTION
99
2.8987-3.0802
0.171
355
0.1445
6184
X-RAY DIFFRACTION
99
3.0802-3.318
0.1775
355
0.1405
6237
X-RAY DIFFRACTION
99
3.318-3.6518
0.1567
312
0.1366
6249
X-RAY DIFFRACTION
99
3.6518-4.1799
0.1458
328
0.1373
6186
X-RAY DIFFRACTION
99
4.1799-5.2649
0.1547
305
0.1371
6190
X-RAY DIFFRACTION
98
5.2649-45.2596
0.1973
308
0.1841
6000
X-RAY DIFFRACTION
96
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