3CCF | pdb_00003ccf

Crystal structure of putative methyltransferase (YP_321342.1) from Anabaena variabilis ATCC 29413 at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3CCF/pdb

• Classification: TRANSFERASE
• Organism(s): Trichormus variabilis ATCC 29413
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-25 Released: 2008-03-11 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal structure of putative methyltransferase (YP_321342.1) from Anabaena variabilis ATCC 29413 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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)

Macromolecule Content 

• Total Structure Weight: 63.98 kDa 
• Atom Count: 4,197 
• Modeled Residue Count: 480 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclopropane-fatty-acyl-phospholipid synthase	A, B	279	Trichormus variabilis ATCC 29413	Mutation(s): 0  Gene Names: YP_321342.1, Ava_0823 EC: 2.1.1.144
UniProt
Find proteins for Q3MEY9 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3MEY9  Go to UniProtKB:  Q3MEY9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEZ	C [auth A], D [auth B]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N

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: 1.90 Å
• R-Value Free:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33CCF

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.83	α = 90
b = 67.23	β = 90
c = 131.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-11 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-03-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary