1VKF | pdb_00001vkf

CRYSTAL STRUCTURE OF A GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELATED PROTEIN (TM1436) FROM THERMOTOGA MARITIMA MSB8 AT 1.65 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VKF/pdb

• Classification: TRANSCRIPTION
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-05-13 Released: 2004-05-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.211 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of Glycerol uptake operon antiterminator-related protein (TM1436) from Thermotoga maritima at 1.65 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 84.56 kDa 
• Atom Count: 5,716 
• Modeled Residue Count: 690 
• Deposited Residue Count: 752 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerol uptake operon antiterminator-related protein	A, B, C, D	188	Thermotoga maritima MSB8	Mutation(s): 4  Gene Names: TM1436
UniProt
Find proteins for Q9X1F0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1F0  Go to UniProtKB:  Q9X1F0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A], G [auth C], H [auth D]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
PO4	F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.211 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VKF

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.527	α = 90
b = 138.783	β = 90
c = 160.626	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary