3HH1 | pdb_00003hh1

The Structure of a Tetrapyrrole methylase family protein domain from Chlorobium tepidum TLS

• PDB DOI: https://doi.org/10.2210/pdb3HH1/pdb

• Classification: TRANSFERASE
• Organism(s): Chlorobaculum tepidum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-14 Released: 2009-07-07 
• Deposition Author(s): Cuff, M.E., Sather, A., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.227 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

The Structure of a Tetrapyrrole methylase family protein domain from Chlorobium tepidum TLS.

Cuff, M.E., Sather, A., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.45 kDa 
• Atom Count: 3,559 
• Modeled Residue Count: 438 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrapyrrole methylase family protein	A, B, C, D	117	Chlorobaculum tepidum	Mutation(s): 0  Gene Names: CT1646 EC: 2.1.1.198
UniProt
Find proteins for Q8KBY6 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)) Explore Q8KBY6  Go to UniProtKB:  Q8KBY6

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.227 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.986	α = 90
b = 47.569	β = 91
c = 64.497	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Cuff, M.E., Sather, A., Clancy, S., 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: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary