2IML | pdb_00002iml

Crystal structure of a hypothetical protein from Archaeoglobus fulgidus binding riboflavin 5'-phosphate

• PDB DOI: https://doi.org/10.2210/pdb2IML/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-10-04 Released: 2006-10-17 
• Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Adams, J., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of a hypothetical protein from Archaeoglobus fulgidus binding riboflavin 5'-phosphate

Bonanno, J.B., Dickey, M., Bain, K.T., Adams, J., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.49 kDa 
• Atom Count: 7,147 
• Modelled Residue Count: 768 
• Deposited Residue Count: 796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B, C, D	199	Archaeoglobus fulgidus	Mutation(s): 4  Gene Names: AF_1834
UniProt
Find proteins for O28442 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28442  Go to UniProtKB:  O28442

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], M [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
GOL	F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], N [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.042	α = 90
b = 103.182	β = 97.01
c = 103.842	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Adams, J., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-10-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2018-11-14
  Changes: Advisory, Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-10-30
  Changes: Advisory, Data collection, Database references, Structure summary