3HM2 | pdb_00003hm2

Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferase Targeted Domain from Corynebacterium diphtheriae

• PDB DOI: https://doi.org/10.2210/pdb3HM2/pdb

• Classification: TRANSFERASE
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-05-28 Released: 2009-07-07 
• Deposition Author(s): Kim, Y., Bigelow, L., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.260 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferase Targeted Domain from Corynebacterium diphtheriae

Kim, Y., Bigelow, L., Keigher, L., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 153.83 kDa 
• Atom Count: 10,700 
• Modeled Residue Count: 1,353 
• Deposited Residue Count: 1,424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
precorrin-6Y C5,15-methyltransferase	A, B, C, D, E, F, G, H	178	Corynebacterium diphtheriae	Mutation(s): 0  Gene Names: DIP1236
UniProt
Find proteins for Q6NHA4 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NHA4  Go to UniProtKB:  Q6NHA4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	I [auth A], L [auth D], M [auth F]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	K [auth D], O [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	J [auth B], N [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.260 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.782	α = 90
b = 113.853	β = 90.12
c = 84.65	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Kim, Y., Bigelow, L., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary