5DGX | pdb_00005dgx

1.73 Angstrom resolution crystal structure of the ABC-ATPase domain (residues 357-609) of lipid A transport protein (msbA) from Francisella tularensis subsp. tularensis SCHU S4 in complex with ADP

PDB DOI: https://doi.org/10.2210/pdb5DGX/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Francisella tularensis subsp. tularensis FSC198
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-08-28 Released: 2015-09-16
Deposition Author(s): Halavaty, A.S., Minasov, G., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.233 (Depositor), 0.240 (DCC)
R-Value Work:
0.194 (Depositor), 0.205 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

1.73 Angstrom resolution crystal structure of the ABC-ATPase domain (residues 357-609) of lipid A transport protein (msbA) from Francisella tularensis subsp. tularensis SCHU S4 in complex with ADP

Halavaty, A.S., Minasov, G., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 28.27 kDa
Atom Count: 2,064
Modeled Residue Count: 233
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid A export ATP-binding/permease protein MsbA	A	256	Francisella tularensis subsp. tularensis FSC198	Mutation(s): 0 Gene Names: msbA, FTF0109 EC: 3.6.3 (PDB Primary Data), 7.5.2.6 (UniProt)
UniProt
Find proteins for Q14JW6 (Francisella tularensis subsp. tularensis (strain FSC 198)) Explore Q14JW6 Go to UniProtKB: Q14JW6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14JW6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.233 (Depositor), 0.240 (DCC)
R-Value Work: 0.194 (Depositor), 0.205 (DCC)
R-Value Observed: 0.196 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.597	α = 90
b = 70.886	β = 103.77
c = 46.647	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing
Coot	model building
ARP	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-09-16

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2015-09-16
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.