- PDB-4v33: Crystal structure of the putative polysaccharide deacetylase BA03... -
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Basic information
Entry
Database: PDB / ID: 4v33
Title
Crystal structure of the putative polysaccharide deacetylase BA0330 from bacillus anthracis
Components
POLYSACCHARIDE DEACETYLASE-LIKE PROTEIN
Keywords
HYDROLASE / FIBRONECTIN TYPE III DOMAIN
Function / homology
Function and homology information
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding Similarity search - Function
SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.
Resolution: 1.48→48.021 Å / SU ML: 0.14 / σ(F): 1.99 / Phase error: 17.11 / Stereochemistry target values: ML / Details: RESIDUES 1-44 WERE NOT LOCATED IN THE EXPERIMENT
Rfactor
Num. reflection
% reflection
Rfree
0.1748
14922
5 %
Rwork
0.1565
-
-
obs
0.1574
155203
94.32 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 25.2 Å2
Refinement step
Cycle: LAST / Resolution: 1.48→48.021 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5070
0
34
942
6046
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.01
5279
X-RAY DIFFRACTION
f_angle_d
1.024
7132
X-RAY DIFFRACTION
f_dihedral_angle_d
12.65
2009
X-RAY DIFFRACTION
f_chiral_restr
0.07
791
X-RAY DIFFRACTION
f_plane_restr
0.005
905
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.4798-1.4966
0.2921
459
0.2799
8819
X-RAY DIFFRACTION
86
1.4966-1.5142
0.286
481
0.2619
9159
X-RAY DIFFRACTION
92
1.5142-1.5326
0.2693
503
0.2522
9465
X-RAY DIFFRACTION
93
1.5326-1.552
0.2532
482
0.2333
9154
X-RAY DIFFRACTION
93
1.552-1.5725
0.2289
500
0.2258
9477
X-RAY DIFFRACTION
93
1.5725-1.594
0.2335
484
0.2096
9320
X-RAY DIFFRACTION
93
1.594-1.6168
0.2222
503
0.1961
9467
X-RAY DIFFRACTION
94
1.6168-1.6409
0.1967
497
0.1855
9452
X-RAY DIFFRACTION
94
1.6409-1.6666
0.1905
484
0.1843
9387
X-RAY DIFFRACTION
94
1.6666-1.6939
0.1982
494
0.1868
9562
X-RAY DIFFRACTION
94
1.6939-1.7231
0.2171
495
0.1896
9400
X-RAY DIFFRACTION
94
1.7231-1.7544
0.2069
494
0.1756
9534
X-RAY DIFFRACTION
95
1.7544-1.7882
0.1807
499
0.1721
9553
X-RAY DIFFRACTION
94
1.7882-1.8247
0.1899
493
0.1655
9429
X-RAY DIFFRACTION
95
1.8247-1.8644
0.1627
499
0.155
9505
X-RAY DIFFRACTION
95
1.8644-1.9077
0.18
509
0.1512
9604
X-RAY DIFFRACTION
95
1.9077-1.9554
0.1702
503
0.1475
9530
X-RAY DIFFRACTION
95
1.9554-2.0083
0.1689
503
0.1485
9633
X-RAY DIFFRACTION
95
2.0083-2.0674
0.1772
495
0.1523
9516
X-RAY DIFFRACTION
96
2.0674-2.1341
0.1783
509
0.158
9622
X-RAY DIFFRACTION
96
2.1341-2.2104
0.1647
508
0.1484
9637
X-RAY DIFFRACTION
96
2.2104-2.2989
0.1713
507
0.1474
9667
X-RAY DIFFRACTION
96
2.2989-2.4035
0.1664
503
0.138
9545
X-RAY DIFFRACTION
96
2.4035-2.5302
0.1768
502
0.1499
9580
X-RAY DIFFRACTION
95
2.5302-2.6888
0.1615
518
0.1517
9685
X-RAY DIFFRACTION
96
2.6888-2.8963
0.1601
491
0.1522
9500
X-RAY DIFFRACTION
95
2.8963-3.1878
0.1735
512
0.1532
9612
X-RAY DIFFRACTION
95
3.1878-3.6489
0.1671
497
0.1468
9570
X-RAY DIFFRACTION
95
3.6489-4.5966
0.1471
498
0.1278
9577
X-RAY DIFFRACTION
95
4.5966-48.0468
0.1516
500
0.1409
9612
X-RAY DIFFRACTION
96
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.9154
0.3458
-1.4735
0.6418
-1.1285
3.0383
-0.1935
-0.3016
-0.1718
0.0191
-0.0267
-0.0951
0.2688
0.3665
0.2004
0.1976
0.0275
0.0214
0.3013
0.0373
0.1511
3.6759
33.3366
62.2485
2
1.791
0.0471
0.5965
1.2988
0.2835
2.0483
-0.0178
0.0421
0.0989
-0.1199
0.0595
0.0638
-0.1575
0.0136
-0.0361
0.1055
-0.0476
0.0148
0.1233
-0.0022
0.1166
7.1429
50.755
32.2788
3
1.5114
0.5234
0.0044
0.9631
-0.3373
1.1946
0.0593
-0.1976
0.0705
0.0872
-0.0701
0.0239
-0.0903
0.0958
0.0127
0.1202
-0.0316
0.0211
0.1617
-0.0199
0.0841
18.1072
54.973
36.1181
4
1.2018
-0.4052
-0.3242
1.6896
-0.3885
0.475
0.2525
0.2834
-0.2473
-0.5463
-0.0293
0.438
0.2648
-0.1484
-0.0749
0.2781
-0.0283
-0.1219
0.1211
-0.0373
0.2723
-29.926
31.5403
-5.0991
5
1.083
0.4502
0.0898
0.5817
-0.0818
0.5533
0.0069
-0.0364
0.0217
-0.0004
-0.0158
0.0346
-0.0046
0.0119
0.0085
0.1136
-0.0038
0.0001
0.0674
-0.0043
0.107
-9.7821
36.2525
11.6091
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAIN 'A' AND (RESID45THROUGH149 )
2
X-RAY DIFFRACTION
2
CHAIN 'A' AND (RESID150THROUGH198 )
3
X-RAY DIFFRACTION
3
CHAIN 'A' AND (RESID199THROUGH360 )
4
X-RAY DIFFRACTION
4
CHAIN 'B' AND (RESID45THROUGH179 )
5
X-RAY DIFFRACTION
5
CHAIN 'B' AND (RESID180THROUGH360 )
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