3LL7 | pdb_00003ll7

Crystal structure of putative methyltransferase PG_1098 from Porphyromonas gingivalis W83

• PDB DOI: https://doi.org/10.2210/pdb3LL7/pdb

• Classification: TRANSFERASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-28 Released: 2010-02-16 
• Deposition Author(s): Chang, C., Chhor, G., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.209 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Crystal structure of putative methyltransferase PG_1098 from Porphyromonas gingivalis W83

Chang, C., Chhor, G., Buck, K., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 46.83 kDa 
• Atom Count: 3,742 
• Modeled Residue Count: 401 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase	A	410	Porphyromonas gingivalis	Mutation(s): 0  Gene Names: PG_1098
UniProt
Find proteins for Q7MVG6 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MVG6  Go to UniProtKB:  Q7MVG6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	D [auth A], E [auth A], F [auth A], I [auth A], J [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.209 (Depositor), 0.222 (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 = 53.132	α = 90
b = 78.485	β = 104.65
c = 64.063	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-16 
Deposition Author(s): Chang, C., Chhor, G., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-02-16
  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: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary