Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 34.01 kDa 
• Atom Count: 2954 
• Residue Count: 292 
• Unique protein chains: 1

3G46

Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloroform bound to the XE4 cavity

• DOI: 10.2210/pdb3G46/pdb

• Classification: OXYGEN BINDING
• Organism(s): Scapharca inaequivalvis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-03 Released: 2009-12-01 
• Deposition Author(s): Knapp, J.E., Pahl, R., Cohen, J., Nichols, J.C., Schulten, K., Gibson, Q.H., Srajer, V., Royer Jr., W.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.91 Å
• R-Value Free: 0.155 
• R-Value Work: 0.129 
• R-Value Observed: 0.129 

Literature

Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis.

Knapp, J.E., Pahl, R., Cohen, J., Nichols, J.C., Schulten, K., Gibson, Q.H., Srajer, V., Royer, W.E.

(2009) Structure 17: 1494-1504

• PubMed: 19913484 
• DOI: 10.1016/j.str.2009.09.004
• Primary Citation of Related Structures:  
  3G4Y, 3G4Q, 3G52, 3G4R, 3G53, 3G4U, 3G4V, 3G4W, 3G46


• PubMed Abstract: 
  

As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computational analysis presented here, reveal protein cavities as potential ligand migration routes. Time-resolved crystallographic experiments show that photodissociated carbon monoxide (CO) docks within 5 ns at the distal pocket B site and at more remote Xe4 and Xe2 cavities. CO rebinding is not affected by the presence of dichloroethane within the major Xe4 protein cavity, demonstrating that this cavity is not on the major exit pathway. The crystal lattice has a substantial influence on ligand migration, suggesting that significant conformational rearrangements may be required for ligand exit. Taken together, these results are consistent with a distal histidine gate as one important ligand entry and exit route, despite its participation in the dimeric interface.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Pharmacology, The University of Massachusetts Medical School, Worcester, MA 01605, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Globin-1	A, B	146	Scapharca inaequivalvis	Mutation(s): 0  Gene Names: HBI
Find proteins for P02213 (Anadara inaequivalvis) Explore P02213  Go to UniProtKB:  P02213

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
XE	A, B	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
CMO	A, B	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.91 Å
• R-Value Free: 0.155 
• R-Value Work: 0.129 
• R-Value Observed: 0.129 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.536	α = 90
b = 43.487	β = 122.25
c = 82.853	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-03 
• Released Date: 2009-12-01 
Deposition Author(s): Knapp, J.E., Pahl, R., Cohen, J., Nichols, J.C., Schulten, K., Gibson, Q.H., Srajer, V., Royer Jr., W.E.

Revision History 

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Advisory, Data collection, Refinement description