4MLC | pdb_00004mlc

ABC Transporter Substrate-Binding Protein fromDesulfitobacterium hafniense

• PDB DOI: https://doi.org/10.2210/pdb4MLC/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Desulfitobacterium hafniense DCB-2
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-09-06 Released: 2013-09-18 
• Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.219 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

ABC Transporter Substrate-Binding Protein fromDesulfitobacterium hafniense

Kim, Y., Chhor, G., Endres, M., 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.49 kDa 
• Atom Count: 2,665 
• Modelled Residue Count: 336 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular ligand-binding receptor	A	356	Desulfitobacterium hafniense DCB-2	Mutation(s): 0  Gene Names: Dhaf_0110
UniProt
Find proteins for B8FZ96 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8FZ96  Go to UniProtKB:  B8FZ96

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.219 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.195	α = 90
b = 81.796	β = 90
c = 128.739	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary