- PDB-3oo7: Crystal structures and biochemical characterization of the bacter... -
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Basic information
Entry
Database: PDB / ID: 3oo7
Title
Crystal structures and biochemical characterization of the bacterial solute receptor AcbH reveal an unprecedented exclusive substrate preference for b-D-galactopyranose
Components
ABC transporter binding protein AcbH
Keywords
SUGAR BINDING PROTEIN / class 2 SBP fold / ABC transporter extracellular solute binding protein / D-galactose Binding
Function / homology
Function and homology information
hydrolase activity, acting on glycosyl bonds / xylan catabolic process / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.91841 Å / Relative weight: 1
Reflection
Number: 192262 / Rmerge(I) obs: 0.158 / D res high: 1.96 Å / Num. obs: 26593 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
Num. obs
% possible obs (%)
ID
Rmerge(I) obs
1.96
2.01
1910
100
1
0.759
2.01
2.07
1898
100
1
0.629
2.07
2.13
1817
100
1
0.556
2.13
2.19
1788
99.9
1
0.452
2.19
2.26
1732
100
1
0.4
2.26
2.34
1676
100
1
0.358
2.34
2.43
1626
100
1
0.317
2.43
2.53
1554
100
1
0.286
2.53
2.64
1525
100
1
0.257
2.64
2.77
1424
100
1
0.203
2.77
2.92
1365
99.9
1
0.181
2.92
3.1
1304
100
1
0.14
3.1
3.31
1246
100
1
0.11
3.31
3.58
1147
100
1
0.083
3.58
3.92
1072
100
1
0.069
3.92
4.38
967
100
1
0.057
4.38
5.06
860
100
1
0.054
5.06
6.2
737
100
1
0.058
6.2
8.77
592
100
1
0.042
Reflection
Resolution: 1.96→34.03 Å / Num. obs: 26593 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 23.675 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 14.53
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge F obs
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. possible
Num. unique obs
Rrim(I) all
% possible all
1.96-2.01
0.537
0.759
3.7
13768
1910
1910
0.817
100
2.01-2.07
0.423
0.629
4.5
13795
1898
1898
0.677
100
2.07-2.13
0.351
0.556
5.2
13226
1817
1817
0.598
100
2.13-2.19
0.292
0.452
6.3
13075
1789
1788
0.486
99.9
2.19-2.26
0.252
0.4
7.2
12667
1732
1732
0.43
100
2.26-2.34
0.235
0.358
8
12282
1676
1676
0.385
100
2.34-2.43
0.2
0.317
9.1
11960
1626
1626
0.341
100
2.43-2.53
0.19
0.286
9.9
11354
1554
1554
0.308
100
2.53-2.64
0.167
0.257
10.8
11148
1525
1525
0.276
100
2.64-2.77
0.136
0.203
13
10435
1424
1424
0.219
100
2.77-2.92
0.11
0.181
14.9
9944
1366
1365
0.195
99.9
2.92-3.1
0.081
0.14
18
9480
1304
1304
0.15
100
3.1-3.31
0.063
0.11
22.4
8994
1246
1246
0.118
100
3.31-3.58
0.045
0.083
27.1
8254
1147
1147
0.09
100
3.58-3.92
0.036
0.069
31.5
7681
1072
1072
0.074
100
3.92-4.38
0.029
0.057
35.5
6844
967
967
0.062
100
4.38-5.06
0.03
0.054
35.5
6051
860
860
0.058
100
5.06-6.2
0.034
0.058
31
5148
737
737
0.063
100
6.2-8.77
0.037
0.042
34.1
3996
592
592
0.046
100
8.77
0.018
0.03
42.2
2160
361
353
0.033
97.8
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Processing
Software
Name
Version
Classification
NB
XSCALE
datascaling
REFMAC
refinement
PDB_EXTRACT
3.1
dataextraction
ADSC
Quantum
datacollection
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: model from SeMet SAD phasing Resolution: 2.1→33.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.91 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21994
1086
5 %
RANDOM
Rwork
0.16412
-
-
-
obs
0.1669
20648
100 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 17.785 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.1 Å2
0 Å2
0 Å2
2-
-
0.23 Å2
0 Å2
3-
-
-
-0.13 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→33.58 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3039
0
56
308
3403
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
3174
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.248
1.95
4312
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.034
5
389
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.236
25.347
144
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.452
15
496
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.472
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.107
0.2
457
X-RAY DIFFRACTION
r_gen_planes_refined
0.014
0.021
2425
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.158
1.5
1941
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.844
2
3120
X-RAY DIFFRACTION
r_scbond_it
3.372
3
1233
X-RAY DIFFRACTION
r_scangle_it
4.945
4.5
1192
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.256
78
-
Rwork
0.203
1478
-
obs
-
-
100 %
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