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Yorodumi- PDB-1hmo: THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hmo | ||||||
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Title | THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION | ||||||
Components | HEMERYTHRIN | ||||||
Keywords | OXYGEN TRANSPORT | ||||||
Function / homology | Function and homology information inorganic ion homeostasis / monoatomic cation homeostasis / oxygen carrier activity / iron ion binding Similarity search - Function | ||||||
Biological species | Themiste dyscritum (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Holmes, M.A. / Letrong, I. / Turley, S. / Sieker, L.C. / Stenkamp, R.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1991 Title: Structures of deoxy and oxy hemerythrin at 2.0 A resolution. Authors: Holmes, M.A. / Le Trong, I. / Turley, S. / Sieker, L.C. / Stenkamp, R.E. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985 Title: Active Site Structures of Deoxyhemerythrin and Oxyhemerythrin Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. / Mccallum, J.D. / Sanders-Loehr, J. #2: Journal: J.Am.Chem.Soc. / Year: 1984 Title: Binuclear Iron Complexes in Methemerythrin and Azidomethemerythrin at 2.0-Angstroms Resolution Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1983 Title: Adjustment of Restraints in the Refinement of Methemerythrin and Azidomethemerythrin at 2.0 Angstroms Resolution. Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. #4: Journal: Acta Crystallogr.,Sect.B / Year: 1982 Title: Restrained Least-Squares Refinement of Themiste Dyscritum Methydroxohemerythrin at 2.0 Angstroms Resolution Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. #5: Journal: Nature / Year: 1981 Title: Structure of the Binuclear Iron Complex in Metazidohaemerythrin from Themiste Dyscritum at 2.2 Angstroms Resolution Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. / Sanders-Loehr, J. #6: Journal: J.Biol.Chem. / Year: 1978 Title: Amino Acid Sequence of Hemerythrin from Themiste Dyscritum. Authors: Stenkamp, R.E. / Lammers, P.J. / Brimhall, B. / Hermodson, M.A. #7: Journal: J.Mol.Biol. / Year: 1978 Title: Crystallographic Studies of Azide, Thiocyanate and Perchlorate Complexes of Methemerythrin Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. #8: Journal: Biochemistry / Year: 1978 Title: Structure of Methemerythrin at 2.8-Angstroms Resolution. Computer Graphics Fit of an Averaged Electron Density Map Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. / Mcqueenjunior, J.E. #9: Journal: J.Mol.Biol. / Year: 1976 Title: Structure of Methemerythrin at 5 Angstroms Resolution Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. / Loehr, J.S. #10: Journal: Proc.Natl.Acad.Sci.USA / Year: 1976 Title: Structure of the Iron Complex in Methemerythrin Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. #11: Journal: J.Mol.Biol. / Year: 1975 Title: An X-Ray Crystallographic Study of Hemerythrin Authors: Loehr, J.S. / Meyerhoff, K.N. / Sieker, L.C. / Jensen, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hmo.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hmo.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/1hmo ftp://data.pdbj.org/pub/pdb/validation_reports/hm/1hmo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Atom site foot note | 1: HYDROGEN BONDING WOULD ARGUE FOR INTERCHANGING THE SIDECHAIN N AND O ATOMS OF ASN 40 AND GLN 59. 2: SERINE 64 IS ACETYLATED. / 3: PRO 7 OF EACH CHAIN IS A CIS PROLINE. |
-Components
#1: Protein | Mass: 13368.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Themiste dyscritum (invertebrata) / References: UniProt: P02246 #2: Chemical | ChemComp-ACE / #3: Chemical | ChemComp-FEO / #4: Chemical | ChemComp-OXY / #5: Water | ChemComp-HOH / | Nonpolymer details | THE BINUCLEAR IRON COMPLEX (DESIGNATED FEO BELOW) CONSISTS OF TWO FE ATOMS BRIDGED BY A MU-OXYGEN ...THE BINUCLEAR IRON COMPLEX (DESIGNATED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.65 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: microdialysis | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / Observed criterion σ(F): 2 / Rmerge F obs: 0.029 |
-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2→10 Å /
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refinement | *PLUS Rfactor obs: 0.173 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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