3CYM | pdb_00003cym

Crystal structure of protein BAD_0989 from Bifidobacterium adolescentis

• PDB DOI: https://doi.org/10.2210/pdb3CYM/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bifidobacterium adolescentis ATCC 15703
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-25 Released: 2008-05-27 
• Deposition Author(s): Patskovsky, Y., Ozyurt, S., Freeman, J., Chang, S., Bain, K., 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: 2.10 Å
• R-Value Free: 
  0.294 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Crystal structure of protein BAD_0989 from Bifidobacterium adolescentis.

Patskovsky, Y., Ozyurt, S., Freeman, J., Chang, S., Bain, K., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 50.64 kDa 
• Atom Count: 3,825 
• Modeled Residue Count: 415 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein BAD_0989	A	440	Bifidobacterium adolescentis ATCC 15703	Mutation(s): 0  Gene Names: BAD_0989
UniProt
Find proteins for A1A237 (Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)) Explore A1A237  Go to UniProtKB:  A1A237

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.294 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.163	α = 90
b = 94.422	β = 90
c = 113.196	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Patskovsky, Y., Ozyurt, S., Freeman, J., Chang, S., Bain, K., 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: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, 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