1WPU | pdb_00001wpu

Crystal Structure of the HutP antitermination complex bound to a single stranded region of hut mRNA

• PDB DOI: https://doi.org/10.2210/pdb1WPU/pdb
• NAKB: 1WPU

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


• Deposited: 2004-09-13 Released: 2005-08-30 
• Deposition Author(s): Kumarevel, T.S., Mizuno, H., Kumar, P.K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.238 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the HutP antitermination Complex:Role of divalent metal ions in allosteric activation

Kumarevel, T.S., Mizuno, H., 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.

Macromolecule Content 

• Total Structure Weight: 36.96 kDa 
• Atom Count: 2,936 
• Modeled Residue Count: 308 
• Deposited Residue Count: 308 
• 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	C [auth A], D [auth B]	147	Bacillus subtilis	Mutation(s): 1
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*GP*AP*GP*UP*U)-3'	A [auth C], B [auth D]	7	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.238 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.06	α = 90
b = 76.06	β = 90
c = 133.99	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
CCP4	data scaling
MOLREP	phasing
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-30 
Deposition Author(s): Kumarevel, T.S., Mizuno, H., Kumar, P.K.R.

Revision History  

• Version 1.0: 2005-08-30
  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: Advisory, Refinement description
• Version 1.4: 2021-11-10
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2023-10-25
  Changes: Data collection, Refinement description