3UHB

HBI (R104K) CO bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures.

Ren, Z.Srajer, V.Knapp, J.E.Royer, W.E.

(2012) Proc Natl Acad Sci U S A 109: 107-112

  • DOI: 10.1073/pnas.1109213108
  • Primary Citation of Related Structures:  
    3QOB, 3UGY, 3UGZ, 3UH3, 3UH5, 3UH6, 3UH7, 3UHB, 3UHC, 3UHD, 3UHE, 3UHG, 3UHH, 3UHI, 3UHK, 3UHN, 3UHQ, 3UHR, 3UHS, 3UHT, 3UHU, 3UHV, 3UHW, 3UHX, 3UHY, 3UHZ, 3UI0

  • PubMed Abstract: 
  • Here we present a meta-analysis of a large collection of static structures of a protein in the Protein Data Bank in order to extract the progression of structural events during protein function. We apply this strategy to the homodimeric hemoglobin HbI from Scapharca inaequivalvis ...

    Here we present a meta-analysis of a large collection of static structures of a protein in the Protein Data Bank in order to extract the progression of structural events during protein function. We apply this strategy to the homodimeric hemoglobin HbI from Scapharca inaequivalvis. We derive a simple dynamic model describing how binding of the first ligand in one of the two chemically identical subunits facilitates a second binding event in the other partner subunit. The results of our ultrafast time-resolved crystallographic studies support this model. We demonstrate that HbI functions like a homodimeric mechanical device, such as pliers or scissors. Ligand-induced motion originating in one subunit is transmitted to the other via conserved pivot points, where the E and F' helices from two partner subunits are "bolted" together to form a stable dimer interface permitting slight relative rotation but preventing sliding.


    Organizational Affiliation

    Center for Advanced Radiation Sources, University of Chicago, 9700 South Cass Avenue, Building 434B, Argonne, IL 60439, USA. renz@uchicago.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Globin-1A, B146Anadara inaequivalvisMutation(s): 1 
UniProt
Find proteins for P02213 (Anadara inaequivalvis)
Explore P02213 
Go to UniProtKB:  P02213
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02213
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.1α = 90
b = 43.84β = 121.97
c = 83.39γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-01-18
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description