+Open data
-Basic information
Entry | Database: PDB / ID: 1uvy | ||||||
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Title | HEME-LIGAND TUNNELING IN GROUP I TRUNCATED HEMOGLOBINS | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / LIGAND DIFFUSION / HEME / OXYGEN STORAGE-TRANSPORT complex | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | PARAMECIUM CAUDATUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Milani, M. / Pesce, A. / Ouellet, Y. / Dewilde, S. / Friedman, J. / Ascenzi, P. / Guertin, M. / Bolognesi, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Heme-Ligand Tunneling in Group I Truncated Hemoglobins Authors: Milani, M. / Pesce, A. / Ouellet, Y. / Dewilde, S. / Friedman, J. / Ascenzi, P. / Guertin, M. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uvy.cif.gz | 35.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uvy.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 1uvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/1uvy ftp://data.pdbj.org/pub/pdb/validation_reports/uv/1uvy | HTTPS FTP |
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-Related structure data
Related structure data | 1s56C 1s61C 1uvxC 1dlwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11914.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PARAMECIUM CAUDATUM (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P15160 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-XE / |
#4: Water | ChemComp-HOH / |
Compound details | TRUNCATED HEMOGLOBIN, WITH 116 AMINO ACID RESIDUES PER CHAIN, WITH 1 XE ATOM DIFFUSED THROUGH THE ...TRUNCATED HEMOGLOBIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: AMMONIUM SULPHATE, SODIUM ACETATE, pH 6.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.5 / Method: vapor diffusion / Details: Pesce, A., (2000) EMBO J., 19, 2424. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 4985 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.6 / % possible all: 98.7 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.112 |
Reflection shell | *PLUS % possible obs: 98.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DLW Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 4985 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.39 |