3ILK | pdb_00003ilk

The structure of a probable methylase family protein from Haemophilus influenzae Rd KW20

• PDB DOI: https://doi.org/10.2210/pdb3ILK/pdb

• Classification: structural genomics, unknown function
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-07 Released: 2009-09-01 
• Deposition Author(s): Tan, K., Li, H., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.246 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

The structure of a probable methylase family protein from Haemophilus influenzae Rd KW20

Tan, K., Li, H., Buck, K., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.31 kDa 
• Atom Count: 3,903 
• Modeled Residue Count: 472 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized tRNA/rRNA methyltransferase HI0380	A, B	244	Haemophilus influenzae	Mutation(s): 0  Gene Names: Haemophilus influenzae, HI0380 EC: 2.1.1
UniProt
Find proteins for P44676 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44676  Go to UniProtKB:  P44676

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.246 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.167	α = 90
b = 94.392	β = 90
c = 124.111	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Tan, K., Li, H., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary