3JTF | pdb_00003jtf

The CBS Domain Pair Structure of a magnesium and cobalt efflux protein from Bordetella parapertussis in complex with AMP

• PDB DOI: https://doi.org/10.2210/pdb3JTF/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bordetella parapertussis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-09-11 Released: 2009-12-22 
• Deposition Author(s): Cuff, M.E., Tesar, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.223 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

The CBS Domain Pair Structure of a magnesium and cobalt efflux protein from Bordetella parapertussis in complex with AMP

Cuff, M.E., Tesar, C., Cobb, G., Joachimiak, A.

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: 30.65 kDa 
• Atom Count: 2,269 
• Modeled Residue Count: 249 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnesium and cobalt efflux protein	A, B	129	Bordetella parapertussis	Mutation(s): 0  Gene Names: BPP1138, corC
UniProt
Find proteins for Q7WB69 (Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)) Explore Q7WB69  Go to UniProtKB:  Q7WB69

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], F [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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:  0.223 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.85	α = 90
b = 84.85	β = 90
c = 38.03	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Cuff, M.E., Tesar, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary