7D51

Crystal structure of a truly knotted protein: cyclized YibK from Haemophilus influenzae

• PDB DOI: https://doi.org/10.2210/pdb7D51/pdb

• Classification: TRANSFERASE
• Organism(s): Haemophilus influenzae Rd KW20
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-24 Released: 2021-09-29 
• Deposition Author(s): Sriramoju, M.K., Ko, K.T., Hsu, S.T.D.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.301 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Physico-chemical properties of a truly knotted protein without open ends

Sriramoju, M.K., Ko, K.T., Hsu, S.T.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.37 kDa 
• Atom Count: 2,558 
• Modelled Residue Count: 327 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (cytidine(34)-2'-O)-methyltransferase	A, B	169	Haemophilus influenzae Rd KW20	Mutation(s): 0  Gene Names: trmL, HI_0766 EC: 2.1.1.207
UniProt
Find proteins for P44868 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44868  Go to UniProtKB:  P44868

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.301 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.738	α = 90
b = 68.781	β = 90
c = 84.357	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): Sriramoju, M.K., Ko, K.T., Hsu, S.T.D.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	MOST107-2628-M-001-005-MY3

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description