3BQ9

Crystal structure of predicted nucleotide-binding protein from Idiomarina baltica OS145

• PDB DOI: https://doi.org/10.2210/pdb3BQ9/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Idiomarina baltica OS145
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-19 Released: 2008-01-01 
• Deposition Author(s): Patskovsky, Y., Toro, R., Meyer, A.J., Dickey, M., Eberle, M., Koss, J., Groshong, C., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Crystal Structure of Predicted Nucleotide-Binding Protein from Idiomarina baltica.

Patskovsky, Y., Toro, R., Meyer, A.J., Dickey, M., Eberle, M., Koss, J., Groshong, C., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 103.54 kDa 
• Atom Count: 7,949 
• Modelled Residue Count: 892 
• Deposited Residue Count: 920 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted Rossmann fold nucleotide-binding domain-containing protein	A, B	460	Idiomarina baltica OS145	Mutation(s): 0  Gene Names: OS145_13019

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.415	α = 90
b = 171.857	β = 90
c = 57.362	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-01 
Deposition Author(s): Patskovsky, Y., Toro, R., Meyer, A.J., Dickey, M., Eberle, M., Koss, J., Groshong, C., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-01-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references, Refinement description