5DMH

Crystal structure of a domain of unknown function (DUF1537) from Ralstonia eutropha H16 (H16_A1561), Target EFI-511666, complex with ADP.

• PDB DOI: https://doi.org/10.2210/pdb5DMH/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Cupriavidus necator H16
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-08 Released: 2015-10-28 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.185 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Literature

Crystal structure of a domain of unknown function (DUF1537) from Ralstonia eutropha H16 (H16_A1561), Target EFI-511666, complex with ADP.

Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Chamala, S., Chowdhury, S., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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.

Macromolecule Content

• Total Structure Weight: 95.26 kDa 
• Atom Count: 6,927 
• Modelled Residue Count: 836 
• Deposited Residue Count: 908 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein conserved in bacteria	A, B	454	Cupriavidus necator H16	Mutation(s): 0  Gene Names: H16_A1561 EC: 2.7.1.217
UniProt
Find proteins for Q0KBC8 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)) Explore Q0KBC8  Go to UniProtKB:  Q0KBC8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

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: 1.80 Å
• R-Value Free: 0.185 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.13	α = 90
b = 87.666	β = 90
c = 178.988	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary