1T6Y | pdb_00001t6y

Crystal structure of ADP, AMP, and FMN bound TM379

• PDB DOI: https://doi.org/10.2210/pdb1T6Y/pdb

• Classification: SIGNALING PROTEIN,TRANSFERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-05-07 Released: 2004-08-10 
• Deposition Author(s): Shin, D.H., Wang, W., Kim, R., Yokota, H., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.298 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Crystal structure of ADP bound FAD synthetase

Shin, D.H., Wang, W., Kim, R., Yokota, H., Kim, S.-H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.79 kDa 
• Atom Count: 4,560 
• Modeled Residue Count: 538 
• Deposited Residue Count: 586 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
riboflavin kinase/FMN adenylyltransferase	A, B	293	Thermotoga maritima	Mutation(s): 0  EC: 2.7.7.2 (UniProt), 2.7.1.26 (UniProt)
UniProt
Find proteins for Q9WZW1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZW1  Go to UniProtKB:  Q9WZW1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], H [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
ADP	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP	D [auth A], G [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.298 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.803	α = 90
b = 82.661	β = 116.42
c = 66.717	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-10 
Deposition Author(s): Shin, D.H., Wang, W., Kim, R., Yokota, H., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2004-08-10
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations