- PDB-4ki0: Crystal structure of the maltose-binding protein/maltose transpor... -
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Basic information
Entry
Database: PDB / ID: 4ki0
Title
Crystal structure of the maltose-binding protein/maltose transporter complex in an outward-facing conformation bound to maltohexaose
Components
ABC transporter related protein
Binding-protein-dependent transport systems inner membrane component
Maltose transport system permease protein MalF
Maltose-binding periplasmic protein
Keywords
TRANSPORT PROTEIN / ABC transporter / ATPase Maltodextrin transporter / ATP binding maltodextrin binding / inner membrane
Function / homology
Function and homology information
ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport ...ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / DNA-binding transcription factor binding / periplasmic space / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function
MalF N-terminal region-like / Periplasmic binding protein-like II / D-maltodextrin-binding protein, MBP / MalF N-terminal region-like / MalF N-terminal region-like / Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain ...MalF N-terminal region-like / Periplasmic binding protein-like II / D-maltodextrin-binding protein, MBP / MalF N-terminal region-like / MalF N-terminal region-like / Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain / MalF, N-terminal region, transmembrane helices / MetI-like fold / MetI-like / Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Nucleic acid-binding proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / Periplasmic binding protein-like II / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / D-Maltodextrin-Binding Protein; domain 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Roll / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
alpha-maltotetraose / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-PGV / : / : / Maltose/maltodextrin transport system permease protein MalF / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin transport system permease protein MalG / Maltose/maltodextrin import ATP-binding protein MalK Similarity search - Component
A: ABC transporter related protein B: ABC transporter related protein E: Maltose-binding periplasmic protein F: Maltose transport system permease protein MalF G: Binding-protein-dependent transport systems inner membrane component hetero molecules
Resolution: 2.38→19.82 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 16.662 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22826
5670
5 %
RANDOM
Rwork
0.19207
-
-
-
obs
0.19387
107943
87.88 %
-
all
-
107943
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 85.321 Å2
Baniso -1
Baniso -2
Baniso -3
1-
7.79 Å2
4.95 Å2
5.75 Å2
2-
-
-2.18 Å2
-2.21 Å2
3-
-
-
-2.4 Å2
Refinement step
Cycle: LAST / Resolution: 2.38→19.82 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
14672
0
416
508
15596
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.019
15438
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
15222
X-RAY DIFFRACTION
r_angle_refined_deg
1.063
1.992
20941
X-RAY DIFFRACTION
r_angle_other_deg
0.718
3
35013
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.156
5
1891
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.666
24.22
628
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.376
15
2517
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.284
15
79
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
2403
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
17017
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
3414
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
1.554
5.05
7564
X-RAY DIFFRACTION
r_mcbond_other
1.554
5.05
7563
X-RAY DIFFRACTION
r_mcangle_it
2.48
7.573
9446
X-RAY DIFFRACTION
r_scbond_it
1.616
5.287
7874
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.38→2.441 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.332
285
-
Rwork
0.31
5506
-
obs
-
-
61.12 %
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
0.7279
0.0122
0.1498
2.9669
1.6738
2.4385
0.0497
-0.0036
-0.0977
-0.0912
0.0148
-0.0866
0.4048
0.1126
-0.0644
0.1778
0.0218
-0.0217
0.1484
0.0746
0.1687
-8.4727
-6.0606
3.1861
2
2.7007
-0.8197
-0.8154
2.9669
0.5137
2.1643
0.2487
0.2264
0.2763
-0.702
-0.0745
-0.7586
-0.0765
0.393
-0.1742
0.2184
-0.0275
0.1576
0.2719
0.0722
0.2882
3.6813
11.2161
-4.6093
3
0.9875
-0.3754
-0.1958
1.6495
-0.3279
3.3676
0.1598
0.0978
0.1178
0.1017
-0.1074
0.1773
-0.6498
-0.5496
-0.0524
0.2333
0.1693
-0.0828
0.2711
-0.051
0.2261
-46.6986
64.8462
55.9326
4
0.385
-0.462
-1.0021
1.3065
1.0374
2.9118
-0.0981
0.1315
-0.1515
0.146
-0.2662
0.1875
0.3098
-0.4865
0.3643
0.0826
-0.0828
-0.0618
0.3423
-0.0502
0.2753
-41.7291
39.054
48.583
5
1.0193
-1.3675
-0.867
3.6113
1.9027
3.1625
0.0098
-0.0417
0.1315
0.0478
-0.0546
-0.1585
-0.0072
0.0831
0.0448
0.0336
-0.0421
-0.0626
0.1525
0.042
0.1632
-22.7789
39.4631
39.6572
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 372
2
X-RAY DIFFRACTION
1
A
1501
3
X-RAY DIFFRACTION
1
A
1502
4
X-RAY DIFFRACTION
2
B
2 - 372
5
X-RAY DIFFRACTION
2
B
401
6
X-RAY DIFFRACTION
2
B
402
7
X-RAY DIFFRACTION
3
E
1 - 370
8
X-RAY DIFFRACTION
3
E
401
9
X-RAY DIFFRACTION
4
F
12 - 505
10
X-RAY DIFFRACTION
4
F
601 - 604
11
X-RAY DIFFRACTION
4
F
607
12
X-RAY DIFFRACTION
4
F
609
13
X-RAY DIFFRACTION
4
F
605 - 606
14
X-RAY DIFFRACTION
5
G
8 - 296
15
X-RAY DIFFRACTION
5
G
301 - 304
16
X-RAY DIFFRACTION
5
G
305 - 306
17
X-RAY DIFFRACTION
5
G
307
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