Download MendeleyBypassing the requirement for coupling of ATP binding and hydrolysis in the lipopolysaccharide ABC transporte
Simpson, B., Ruiz, N.Not Published
6MGF | pdb_00006mgf
untagged, wild-type LptB in complex with ADP
- PDB DOI: https://doi.org/10.2210/pdb6MGF/pdb
- Classification: LIPID TRANSPORT
- Organism(s): Escherichia coli K-12
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2018-09-13 Released: 2019-09-18
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.98 Å
- R-Value Free: 0.237 (Depositor), 0.240 (DCC)
- R-Value Work: 0.201 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.205 (Depositor)
Starting Model: experimental
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This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Lipopolysaccharide export system ATP-binding protein LptB | 241 | Escherichia coli K-12 | Mutation(s): 0 Gene Names: lptB, yhbG, b3201, JW3168 EC: 3.6.3 (PDB Primary Data), 7.5.2 (UniProt) |  | |
UniProt | |||||
Find proteins for P0A9V1 (Escherichia coli (strain K12)) Explore P0A9V1 Go to UniProtKB: P0A9V1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0A9V1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CZJ Query on CZJ | D [auth A] | (3s,5s,7s)-N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-beta-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-1-ben
zopyran-3-yl}tricyclo[3.3.1.1~3,7~]decane-1-carboxamide C30 H38 N2 O10 SFCPIJFPMNEBLW-GGTPUZHSSA-N |  | ||
| ADP Query on ADP | C [auth A] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N |  | ||
| MG Query on MG | B [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.98 Å
- R-Value Free: 0.237 (Depositor), 0.240 (DCC)
- R-Value Work: 0.201 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.205 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 102.742 | α = 90 |
| b = 34.767 | β = 100.07 |
| c = 62.897 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Aimless | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-09-18 Deposition Author(s): Mandler, M.D., Owens, T.W., Ruiz, N., Kahne, D.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01 GM066174 |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R01 AI081059 |
Revision History (Full details and data files)
- Version 1.0: 2019-09-18
Type: Initial release - Version 1.1: 2019-12-18
Changes: Author supporting evidence - Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
