2GA1 | pdb_00002ga1

Crystal structure of a duf433 member protein (ava_0674) from anabaena variabilis atcc 29413 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2GA1/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Trichormus variabilis ATCC 29413
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-07 Released: 2006-03-28 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Crystal structure of (YP_321193.1) from Anabaena variabilis ATCC 29413 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 24.16 kDa 
• Atom Count: 1,838 
• Modeled Residue Count: 204 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein of unknown function DUF433	A, B	106	Trichormus variabilis ATCC 29413	Mutation(s): 2  Gene Names: YP_321193.1
UniProt
Find proteins for Q3MFD8 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3MFD8  Go to UniProtKB:  Q3MFD8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.00 Å
• R-Value Free:  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32GA1

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.98	α = 90
b = 65.12	β = 90
c = 86.86	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-28 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-03-28
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary