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Yorodumi- PDB-1emy: CRYSTAL STRUCTURE OF ASIAN ELEPHANT (ELEPHAS MAXIMUS) CYANO-MET M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1emy | ||||||
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Title | CRYSTAL STRUCTURE OF ASIAN ELEPHANT (ELEPHAS MAXIMUS) CYANO-MET MYOGLOBIN AT 1.78 ANGSTROMS RESOLUTION. PHE 29 (B10) ACCOUNTS FOR ITS UNUSUAL LIGAND BINDING PROPERTIES | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / HEME PROTEIN / GLOBIN FOLD | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Elephas maximus (Asiatic elephant) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.78 Å | ||||||
Authors | Bisig, D.A. / Piontek, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1995 Title: Crystal structure of Asian elephant (Elephas maximus) cyano-metmyoglobin at 1.78-A resolution. Phe29(B10) accounts for its unusual ligand binding properties. Authors: Bisig, D.A. / Di Iorio, E.E. / Diederichs, K. / Winterhalter, K.H. / Piontek, K. #1: Journal: To be Published Title: A Double Mutant of Sperm Whale Myoglobin Mimics the Structure and Function of Elephant Myoglobin Authors: Zhao, X. / Vyas, K. / Nguyen, B.D. / Rajarathnam, K. / La Mar, G.N. / Li, T. / Phillips Jr., G.N. / Eich, R.F. / Olson, J.S. / Ling, J. / Bocian, D.F. #2: Journal: J.Biol.Chem. / Year: 1993 Title: 1H NMR Investigation of the Heme Cavity of Elephant (E7 Gln) met-Cyano-Myoglobin. Evidence for a B-Helix Phenylalanine Interaction with Bound Ligand Authors: Vyas, K. / Rajarathnam, K. / Yu, L.P. / Emerson, S.D. / La Mar, G.N. / Krishnamoorthi, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1emy.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1emy.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 1emy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/1emy ftp://data.pdbj.org/pub/pdb/validation_reports/em/1emy | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17026.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elephas maximus (Asiatic elephant) / Organ: SKELETALSkeleton / References: UniProt: P02186 |
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#2: Chemical | ChemComp-CYN / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
Compound details | COMPND MET FORM. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.41 % | |||||||||||||||||||||||||
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Crystal grow | Details: CRYSTALLIZATION CONDITIONS METHOD: HANGING DROP VAPOR DIFFUSION PRECIPITANT: 45% PEG 1000 BUFFER: 0.1M TRIS/HCL PH: 8.5 SALT: 0.15M MAGNESIUM ACETATE PROTEIN CONCENTRATION: 10MG/ML ...Details: CRYSTALLIZATION CONDITIONS METHOD: HANGING DROP VAPOR DIFFUSION PRECIPITANT: 45% PEG 1000 BUFFER: 0.1M TRIS/HCL PH: 8.5 SALT: 0.15M MAGNESIUM ACETATE PROTEIN CONCENTRATION: 10MG/ML TEMPERATURE: 293K CRYSTAL SIZE: 0.8 X 0.4 X 0.3 MM | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, hanging drop / Details: macroseeding | |||||||||||||||||||||||||
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 | Num. obs: 13649 / % possible obs: 93.6 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Highest resolution: 1.78 Å / Redundancy: 5 % / Num. measured all: 68768 / Rmerge(I) obs: 0.045 |
-Processing
Software |
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Refinement | Resolution: 1.78→8 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 21.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→8 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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