4MPT | pdb_00004mpt

Crystal Structure of Periplasmic binding Protein Type 1 from Bordetella pertussis Tohama I

• PDB DOI: https://doi.org/10.2210/pdb4MPT/pdb

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


• Deposited: 2013-09-13 Released: 2013-12-11 
• Deposition Author(s): Kim, Y., Joachimiak, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Crystal Structure of Periplasmic binding Protein Type 1 from Bordetella pertussis Tohama I

Kim, Y., Joachimiak, G., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 82.69 kDa 
• Atom Count: 6,281 
• Modeled Residue Count: 748 
• Deposited Residue Count: 760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative leu/ile/val-binding protein	A, B	380	Bordetella pertussis Tohama I	Mutation(s): 0  Gene Names: BP0622
UniProt
Find proteins for Q7VS30 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VS30  Go to UniProtKB:  Q7VS30

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth A], E [auth B], F [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.75 Å
• R-Value Free:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.565	α = 90
b = 86.565	β = 90
c = 194.053	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
DM	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Kim, Y., Joachimiak, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary