3UP9 | pdb_00003up9

Crystal structure of a putative lipoprotein (ACTODO_00931) from Actinomyces odontolyticus ATCC 17982 at 2.35 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3UP9/pdb

• Classification: METHIONINE-BINDING PROTEIN
• Organism(s): Schaalia dentiphila ATCC 17982
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-17 Released: 2012-01-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.205 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a hypothetical protein ACTODO_00931 (hypothetical protein ACTODO_00931, SP17422A, P_02044074.1) from Actinomyces odontolyticus ATCC 17982 at 2.35 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.78 kDa 
• Atom Count: 2,030 
• Modeled Residue Count: 239 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	245	Schaalia dentiphila ATCC 17982	Mutation(s): 0  Gene Names: ACTODO_00931
UniProt
Find proteins for A7BBB2 (Schaalia dentiphila ATCC 17982) Explore A7BBB2  Go to UniProtKB:  A7BBB2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	G [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
MSE	B [auth A]	SELENOMETHIONINE C5 H11 N O2 Se RJFAYQIBOAGBLC-BYPYZUCNSA-N
PG4	C [auth A], D [auth A], E [auth A], F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.205 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33UP9

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.917	α = 90
b = 95.917	β = 90
c = 93.781	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	refinement
SCALA	data scaling
MolProbity	model building
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection