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PDBsum entry 1vrf
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protein ligands links
Heme protein PDB id
1vrf

 

 

 

 

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Contents
Protein chain
147 a.a. *
Ligands
HEM-CMO
* Residue conservation analysis
PDB id:
1vrf
Name: Heme protein
Title: Solution structure of component iv glycera dibranchiata monomeric hemoglobin-co
Structure: Protein (globin, monomeric component m-iv). Chain: a. Synonym: ghm4. Engineered: yes
Source: Glycera dibranchiata. Organism_taxid: 6350. Tissue: blood. Cell: erythrocyte. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: recombinant protein was produced in e. Coli
NMR struc: 1 models
Authors: B.F.Volkman,S.L.Alam,J.D.Satterlee,J.L.Markley
Key ref:
B.F.Volkman et al. (1998). Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO. Biochemistry, 37, 10906-10919. PubMed id: 9692983 DOI: 10.1021/bi980810b
Date:
25-Mar-99     Release date:   01-Apr-99    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15447  (GLB4_GLYDI) -  Globin, monomeric component M-IV from Glycera dibranchiata
Seq:
Struc: 		148 a.a.
147 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1021/bi980810b Biochemistry 37:10906-10919 (1998)
PubMed id: 9692983  
 
 
Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO.
B.F.Volkman, S.L.Alam, J.D.Satterlee, J.L.Markley.
 
  ABSTRACT  
 
The solution structure and backbone dynamics of the recombinant, ferrous CO-ligated form of component IV monomeric hemoglobin from Glycera dibranchiata (GMH4CO) have been characterized by NMR spectroscopy. Distance geometry and simulated annealing calculations utilizing a total of 2550 distance and torsion angle constraints yielded an ensemble of 29 structures with an overall average backbone rmsd of 0.48 A from the average structure. Differences between the solution structure and a related crystal structure are confined to regions of lower precision in either the NMR or X-ray structure, or in regions where the amino acid sequences differ. 15N relaxation measurements at 76.0 and 60.8 MHz were analyzed with an extended model-free approach, and revealed low-frequency motions in the vicinity of the heme, concentrated in the F helix. Amide proton protection factors were obtained from H-D amide exchange measurements on 15N-labeled protein. Patterns in the backbone dynamics and protection factors were shown to correlate with regions of heterogeneity and disorder in the ensemble of NMR structures and with large crystallographic B-factors in the X-ray structures. Surprisingly, while the backbone atoms of the F helix have higher rmsds and larger measures of dynamics on the microsecond to millisecond time scale than the other helices, amide protection factors for residues in the F helix were observed to be similar to those of the other helices. This contrasts with H-D amide exchange measurements on sperm whale myoglobin which indicated low protection for the F helix (S. N. Loh and B. F. Volkman, unpublished results). These results for GMH4 suggest a model in which the F helix undergoes collective motions as a relatively rigid hydrogen-bonded unit, possibly pivoting about a central position near residue Val87.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16055450 B.M.Potter, L.S.Feng, P.Parasuram, V.A.Matskevich, J.A.Wilson, G.K.Andrews, and J.H.Laity (2005).
The six zinc fingers of metal-responsive element binding transcription factor-1 form stable and quasi-ordered structures with relatively small differences in zinc affinities.
  J Biol Chem, 280, 28529-28540.  
15635690 J.T.Schuman, J.S.Grinstead, V.Apostolopoulos, and A.P.Campbell (2005).
Structural and dynamic consequences of increasing repeats in a MUC1 peptide tumor antigen.
  Biopolymers, 77, 107-120.  
16042389 Z.Ding, G.I.Lee, X.Liang, F.Gallazzi, A.Arunima, and S.R.Van Doren (2005).
PhosphoThr peptide binding globally rigidifies much of the FHA domain from Arabidopsis receptor kinase-associated protein phosphatase.
  Biochemistry, 44, 10119-10134.  
12557184 C.González, J.L.Neira, S.Ventura, S.Bronsoms, M.Rico, and F.X.Avilés (2003).
Structure and dynamics of the potato carboxypeptidase inhibitor by 1H and 15N NMR.
  Proteins, 50, 410-422.
PDB code: 1h20
14640698 J.S.Grinstead, J.T.Schuman, and A.P.Campbell (2003).
Epitope mapping of antigenic MUC1 peptides to breast cancer antibody fragment B27.29: a heteronuclear NMR study.
  Biochemistry, 42, 14293-14305.  
11839303 C.A.Andersen, A.G.Palmer, S.Brunak, and B.Rost (2002).
Continuum secondary structure captures protein flexibility.
  Structure, 10, 175-184.  
12211015 H.J.Park, C.Yang, N.Treff, J.D.Satterlee, and C.Kang (2002).
Crystal structures of unligated and CN-ligated Glycera dibranchiata monomer ferric hemoglobin components III and IV.
  Proteins, 49, 49-60.
PDB codes: 1jf3 1jf4 1jl6 1jl7
10684619 D.C.Yeh, M.V.Thorsteinsson, D.R.Bevan, M.Potts, and G.N.La Mar (2000).
Solution 1H NMR study of the heme cavity and folding topology of the abbreviated chain 118-residue globin from the cyanobacterium Nostoc commune.
  Biochemistry, 39, 1389-1399.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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