- PDB-2r6g: The Crystal Structure of the E. coli Maltose Transporter -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2r6g
Title
The Crystal Structure of the E. coli Maltose Transporter
Components
(Maltose transport system permease protein ...) x 2
Maltose-binding periplasmic protein
Maltose/maltodextrin import ATP-binding protein malK
Keywords
HYDROLASE/TRANSPORT PROTEIN / ABC transporter / catalytic intermediate / E. coli maltose transporter / MBP / maltodextrin binding protein / MalK / ATP binding cassette / ATP-binding / Hydrolase / Inner membrane / Membrane / Nucleotide-binding / Sugar transport / Transmembrane / HYDROLASE-TRANSPORT PROTEIN COMPLEX
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 / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding ...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 / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / 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 / 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-maltose / ADENOSINE-5'-TRIPHOSPHATE / 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 / Maltose/maltodextrin import ATP-binding protein MalK Similarity search - Component
A: Maltose/maltodextrin import ATP-binding protein malK B: Maltose/maltodextrin import ATP-binding protein malK E: Maltose-binding periplasmic protein F: Maltose transport system permease protein malF G: Maltose transport system permease protein malG hetero molecules
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 30, 2007 Details: Si(111) Double Crystal Monochromator. Adjustable focusing mirrors in K-B geometry
Radiation
Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0332 Å / Relative weight: 1
Reflection
Redundancy: 3.6 % / Av σ(I) over netI: 8.3 / Number: 236250 / Rmerge(I) obs: 0.092 / Χ2: 1.09 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 66520 / % possible obs: 91.4
Resolution: 2.8→47.4 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.899 / SU B: 40.785 / SU ML: 0.361 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2714
1185
2 %
RANDOM
Rwork
0.24164
-
-
-
obs
0.24223
58103
83.76 %
-
all
-
59288
-
-
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: 83.877 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.95 Å2
3.16 Å2
5.32 Å2
2-
-
-2.54 Å2
-2.06 Å2
3-
-
-
-4.16 Å2
Refinement step
Cycle: LAST / Resolution: 2.8→47.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
14628
0
85
0
14713
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
15045
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
0.974
1.975
20472
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.468
5
1880
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.758
24.226
620
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.378
15
2500
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.172
15
77
X-RAY DIFFRACTION
r_chiral_restr
0.064
0.2
2353
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
11236
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.176
0.2
7470
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.296
0.2
10425
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.107
0.2
480
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
0.167
0.2
49
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.075
0.2
1
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
0.143
1.5
9633
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.257
2
15112
X-RAY DIFFRACTION
r_scbond_it
0.228
3
6172
X-RAY DIFFRACTION
r_scangle_it
0.386
4.5
5360
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.8→2.873 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.36
50
-
Rwork
0.33
2595
-
obs
-
-
50.88 %
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
1.9962
1.2838
-0.2976
1.0661
0.2271
0.7725
-0.2078
0.0363
0.4193
0.098
-0.1309
0.1414
0.6217
-0.416
0.3388
0.4562
0.0772
0.0141
0.3815
0.0974
0.4217
-19.1057
-10.7549
16.9514
2
0.7457
0.018
-0.0388
2.6038
1.1215
1.766
0.047
-0.0461
-0.0949
-0.1339
0.018
-0.2325
0.1959
0.1322
-0.065
0.253
0.0252
0.0124
0.1977
0.0691
0.311
-5.3096
-6.5731
4.1614
3
2.4113
0.1754
-0.5709
1.985
0.4028
1.7676
0.065
0.131
0.0613
-0.4957
0.0388
-0.3526
-0.3049
0.1072
-0.1038
0.4077
-0.0089
0.1037
0.1254
0.0746
0.2167
-1.4199
16.5103
-1.7983
4
3.5525
2.2461
-0.1951
4.2545
-0.908
2.254
0.0862
0.0665
-0.3202
-0.3212
0.0182
-1.5628
0.0472
0.7272
-0.1044
0.3746
0.0571
0.3017
0.3488
-0.1001
0.683
20.9404
-2.4292
-3.8597
5
0.9323
-0.341
0.0436
1.1543
-0.5436
2.5576
0.1567
0.1595
0.139
-0.0124
-0.0271
0.0828
-0.5914
-0.5183
-0.1296
0.3639
0.1436
0.0426
0.1879
0.0274
0.2008
-46.7367
62.9382
57.4496
6
0.009
0.0269
-0.0265
0.0803
-0.0791
0.0779
0.1708
-1.0568
-0.6655
1.2004
0.3481
-0.1393
0.9148
0.8805
-0.5189
0.6082
-0.0037
0.0003
0.6029
0.0009
0.6091
-30.5084
11.6427
61.1635
7
0.3068
-0.2984
-0.6275
1.067
0.9559
2.3398
-0.1646
0.1153
-0.1377
0.4212
-0.1628
0.3068
0.4401
-0.4631
0.3274
0.4149
-0.1275
0.0813
0.203
-0.0206
0.3001
-50.0034
38.156
78.234
8
0.516
-0.3936
-0.9525
1.2247
0.4974
2.5526
0.1879
0.2219
0.0234
-0.291
-0.1988
0.0963
-0.1684
-0.5437
0.011
0.1841
0.0396
-0.0569
0.3063
0.0252
0.1857
-35.1483
41.3893
27.7415
9
1.7327
-0.6699
0.3052
3.9694
-1.5705
0.9065
-0.2562
0.1873
-0.0907
-0.5825
-0.1176
0.0035
0.0543
-0.5816
0.3739
0.1028
-0.0726
-0.0579
0.5366
-0.0815
0.2143
-51.0955
41.44
38.5284
10
0.8512
-0.6095
-0.7687
2.3597
1.0977
2.5413
0.0953
0.1513
0.0623
-0.0867
-0.0693
0.0398
-0.1099
-0.0862
-0.0259
0.137
-0.048
-0.0492
0.277
0.0749
0.3593
-24.8038
42.7013
39.4226
11
0.8492
-0.9237
-0.7261
1.832
1.3672
2.15
0.0148
-0.0588
0.0354
0.1533
-0.0453
-0.0548
0.2117
-0.0167
0.0305
0.2539
-0.0509
-0.0424
0.2686
0.0651
0.3155
-22.1271
31.8035
41.7299
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
2 - 29
2 - 29
2
X-RAY DIFFRACTION
2
A
A
30 - 372
30 - 372
3
X-RAY DIFFRACTION
3
B
B
2 - 267
2 - 267
4
X-RAY DIFFRACTION
4
B
B
268 - 373
268 - 373
5
X-RAY DIFFRACTION
5
E
C
1 - 370
1 - 370
6
X-RAY DIFFRACTION
6
F
D
13 - 53
13 - 53
7
X-RAY DIFFRACTION
7
F
D
54 - 248
54 - 248
8
X-RAY DIFFRACTION
8
F
D
249 - 441
249 - 441
9
X-RAY DIFFRACTION
9
F
D
442 - 504
442 - 504
10
X-RAY DIFFRACTION
10
G
E
7 - 145
7 - 145
11
X-RAY DIFFRACTION
11
G
E
146 - 296
146 - 296
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi