1TT7 | pdb_00001tt7

Crystal structure of Bacillus subtilis protein yhfP

• PDB DOI: https://doi.org/10.2210/pdb1TT7/pdb

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


• Deposited: 2004-06-22 Released: 2004-12-14 
• 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: 2.70 Å
• R-Value Free: 
  0.262 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

The structural study of Hypothetical protein yhfp

Min, T., Gorman, J., Shapiro, L.

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.

Macromolecule Content 

• Total Structure Weight: 209.86 kDa 
• Atom Count: 14,777 
• Modeled Residue Count: 1,974 
• Deposited Residue Count: 1,980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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

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: 2.70 Å
• R-Value Free:  0.262 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.219	α = 90
b = 133.546	β = 90
c = 166.335	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-14 
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: 2004-12-14
  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: Data collection
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Structure summary