2dn1: Difference between revisions
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|PDB= 2dn1 |SIZE=350|CAPTION= <scene name='initialview01'>2dn1</scene>, resolution 1.25Å | |PDB= 2dn1 |SIZE=350|CAPTION= <scene name='initialview01'>2dn1</scene>, resolution 1.25Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MBN:TOLUENE'>MBN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[2dn2|2DN2]], [[2dn3|2DN3]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dn1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dn1 OCA], [http://www.ebi.ac.uk/pdbsum/2dn1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dn1 RCSB]</span> | |||
}} | }} | ||
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==Overview== | ==Overview== | ||
The most recent refinement of the crystallographic structure of oxyhaemoglobin (oxyHb) was completed in 1983, and differences between this real-space refined model and later R state models have been interpreted as evidence of crystallisation artefacts, or numerous sub-states. We have refined models of deoxy, oxy and carbonmonoxy Hb to 1.25 A resolution each, and compare them with other Hb structures. It is shown that the older structures reflect the software used in refinement, and many differences with newer structures are unlikely to be physiologically relevant. The improved accuracy of our models clarifies the disagreement between NMR and X-ray studies of oxyHb, the NMR experiments suggesting a hydrogen bond to exist between the distal histidine and oxygen ligand of both the alpha and beta-subunits. The high-resolution crystal structure also reveals a hydrogen bond in both subunit types, but with subtly different geometry which may explain the very different behaviour when this residue is mutated to glycine in alpha or beta globin. We also propose a new set of relatively fixed residues to act as a frame of reference; this set contains a similar number of atoms to the well-known "BGH" frame yet shows a much smaller rmsd value between R and T state models of HbA. | The most recent refinement of the crystallographic structure of oxyhaemoglobin (oxyHb) was completed in 1983, and differences between this real-space refined model and later R state models have been interpreted as evidence of crystallisation artefacts, or numerous sub-states. We have refined models of deoxy, oxy and carbonmonoxy Hb to 1.25 A resolution each, and compare them with other Hb structures. It is shown that the older structures reflect the software used in refinement, and many differences with newer structures are unlikely to be physiologically relevant. The improved accuracy of our models clarifies the disagreement between NMR and X-ray studies of oxyHb, the NMR experiments suggesting a hydrogen bond to exist between the distal histidine and oxygen ligand of both the alpha and beta-subunits. The high-resolution crystal structure also reveals a hydrogen bond in both subunit types, but with subtly different geometry which may explain the very different behaviour when this residue is mutated to glycine in alpha or beta globin. We also propose a new set of relatively fixed residues to act as a frame of reference; this set contains a similar number of atoms to the well-known "BGH" frame yet shows a much smaller rmsd value between R and T state models of HbA. | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Tame, J R.]] | [[Category: Tame, J R.]] | ||
[[Category: Yokoyama, T.]] | [[Category: Yokoyama, T.]] | ||
[[Category: high resolution crystal structure]] | [[Category: high resolution crystal structure]] | ||
[[Category: human hemoglobin]] | [[Category: human hemoglobin]] | ||
[[Category: oxygen transport]] | [[Category: oxygen transport]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:36:47 2008'' | ||
Revision as of 02:36, 31 March 2008
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| , resolution 1.25Å | |||||||
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| Ligands: | , , | ||||||
| Related: | 2DN2, 2DN3
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
1.25A resolution crystal structure of human hemoglobin in the oxy form
OverviewOverview
The most recent refinement of the crystallographic structure of oxyhaemoglobin (oxyHb) was completed in 1983, and differences between this real-space refined model and later R state models have been interpreted as evidence of crystallisation artefacts, or numerous sub-states. We have refined models of deoxy, oxy and carbonmonoxy Hb to 1.25 A resolution each, and compare them with other Hb structures. It is shown that the older structures reflect the software used in refinement, and many differences with newer structures are unlikely to be physiologically relevant. The improved accuracy of our models clarifies the disagreement between NMR and X-ray studies of oxyHb, the NMR experiments suggesting a hydrogen bond to exist between the distal histidine and oxygen ligand of both the alpha and beta-subunits. The high-resolution crystal structure also reveals a hydrogen bond in both subunit types, but with subtly different geometry which may explain the very different behaviour when this residue is mutated to glycine in alpha or beta globin. We also propose a new set of relatively fixed residues to act as a frame of reference; this set contains a similar number of atoms to the well-known "BGH" frame yet shows a much smaller rmsd value between R and T state models of HbA.
About this StructureAbout this Structure
2DN1 is a Protein complex structure of sequences from Homo sapiens. This structure supersedes the now removed PDB entry 2DFO. Full crystallographic information is available from OCA.
ReferenceReference
1.25 A resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms., Park SY, Yokoyama T, Shibayama N, Shiro Y, Tame JR, J Mol Biol. 2006 Jul 14;360(3):690-701. Epub 2006 May 30. PMID:16765986
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