4YER | pdb_00004yer

Crystal structure of an ABC transporter ATP-binding protein (TM_1403) from Thermotoga maritima MSB8 at 2.35 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4YER/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-24 Released: 2015-03-11 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Crystal structure of an ABC transporter ATP-binding protein (TM_1403) from Thermotoga maritima MSB8 at 2.35 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 77.51 kDa 
• Atom Count: 4,426 
• Modeled Residue Count: 562 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter ATP-binding protein	A, B	328	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM_1403, THEMA_07300, Tmari_1410
UniProt
Find proteins for Q9X1C3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1C3  Go to UniProtKB:  Q9X1C3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.31	α = 90
b = 101.18	β = 90
c = 110.21	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-03-11 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094586

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2023-02-01
  Changes: Database references
• Version 1.6: 2024-10-30
  Changes: Data collection, Structure summary