1Y9E

Crystal structure of Bacillus subtilis protein yhfP with NAD bound

• PDB DOI: https://doi.org/10.2210/pdb1Y9E/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-12-15 Released: 2004-12-21 
• Deposition Author(s): Min, T., Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Literature

The crystal structure of hypothetical protein yhfP from Bacillus subtilis

Min, T., Gorman, J., Shapiro, L., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 213.84 kDa 
• Atom Count: 14,982 
• Modelled Residue Count: 1,974 
• Deposited Residue Count: 1,980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein yhfP	A, B, C, D, E, F	330	Bacillus subtilis	Mutation(s): 4  Gene Names: yhfP EC: 1.6.5
UniProt
Find proteins for O07615 (Bacillus subtilis (strain 168)) Explore O07615  Go to UniProtKB:  O07615

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.271	α = 90
b = 136.922	β = 90
c = 167.135	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-21 
Deposition Author(s): Min, T., Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-12-21
  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: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2024-10-30
  Changes: Data collection, Database references, Structure summary