3BOY | pdb_00003boy

Crystal structure of the HutP antitermination complex bound to the HUT mRNA

• PDB DOI: https://doi.org/10.2210/pdb3BOY/pdb
• Entry: 3BOY supersedes: 2GZT
• NAKB: 3BOY

• Classification: TRANSCRIPTION/RNA
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-12-18 Released: 2008-01-15 
• Deposition Author(s): Kumarevel, T.S., Balasundaresan, D., Jeyakanthan, J., Shinkai, A., Yokoyama, S., Kumar, P.K.R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.246 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of HutP complexed with the 55-mer RNA

Kumarevel, T., Balasundaresan, D., Jeyakanthan, J., Shinkai, A., Yokoyama, S., Kumar, P.K.R.

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: 55.72 kDa 
• Atom Count: 4,270 
• Modeled Residue Count: 463 
• Deposited Residue Count: 463 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hut operon positive regulatory protein	B [auth A], C [auth B], D [auth C]	147	Bacillus subtilis	Mutation(s): 1  Gene Names: hutP
UniProt
Find proteins for P10943 (Bacillus subtilis (strain 168)) Explore P10943  Go to UniProtKB:  P10943

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*U)-3'	A [auth D]	22	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HIS	F [auth A], G [auth A], H [auth A]	HISTIDINE C6 H10 N3 O2 HNDVDQJCIGZPNO-YFKPBYRVSA-O
MG	E [auth A], I [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.246 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.635	α = 90
b = 76.469	β = 109.06
c = 62.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-15 
Deposition Author(s): Kumarevel, T.S., Balasundaresan, D., Jeyakanthan, J., Shinkai, A., Yokoyama, S., Kumar, P.K.R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 2GZT

Revision History  

• Version 1.0: 2008-01-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2021-11-10
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description