3TD9 | pdb_00003td9

Crystal structure of a Leucine binding protein LivK (TM1135) from Thermotoga maritima MSB8 at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3TD9/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-10 Released: 2011-09-07 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.193 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

Crystal structure of a Leucine binding protein LivK (TM1135) from Thermotoga maritima MSB8 at 1.90 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)

Macromolecule Content 

• Total Structure Weight: 41.28 kDa 
• Atom Count: 3,054 
• Modeled Residue Count: 350 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched chain amino acid ABC transporter, periplasmic amino acid-binding protein	A	366	Thermotoga maritima	Mutation(s): 0  Gene Names: TM1135, TM_1135
UniProt
Find proteins for Q9X0L9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0L9  Go to UniProtKB:  Q9X0L9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHE	B [auth A]	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.193 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33TD9

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.685	α = 90
b = 91.315	β = 90
c = 90.657	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2011-09-21
  Changes: Other
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary