6EEN | pdb_00006een

Crystal structure of a designer Pentatrico Peptide RNA binding protein, bound to a complex RNA target and featuring an infinite superhelix and microheterogeneity.

• PDB DOI: https://doi.org/10.2210/pdb6EEN/pdb
• NAKB: 6EEN

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-15 Released: 2019-08-21 
• Deposition Author(s): Schmidberger, J.W., Bond, C.S.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.248 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a designer Pentatrico Peptide RNA binding protein, bound to a complex RNA target and featuring an infinite superhelix and microheterogeneity.

Schmidberger, J.W., Bond, C.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 151.11 kDa 
• Atom Count: 10,755 
• Modeled Residue Count: 1,296 
• Deposited Residue Count: 1,296 
• Unique protein chains: 4
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Designer Pentatricopeptide Protein dPPR10	A	315	Zea mays	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Designer Pentatricopeptide Protein dPPR10	B	315	Zea mays	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Designer Pentatricopeptide Protein dPPR10	C	315	Zea mays	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Designer Pentatricopeptide Protein dPPR10	D	315	Zea mays	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')	E [auth F]	9	Zea mays

Entity ID: 6
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')	F [auth G]	9	Zea mays

Entity ID: 7
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')	G [auth H]	9	Zea mays

Entity ID: 8
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')	H [auth I]	9	Zea mays

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.248 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.347	α = 118.12
b = 51.647	β = 97.21
c = 51.972	γ = 96

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Schmidberger, J.W., Bond, C.S.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	--

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description