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Yorodumi- PDB-3lqd: Crystal structure determination of Lepus europaeus 2.8 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lqd | ||||||
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Title | Crystal structure determination of Lepus europaeus 2.8 A resolution | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / LEPUS EUROPAEUS / MONOCLINIC / OXYGEN TRANPORT/STORAGE / HEME / IRON / METAL-BINDING / OXYGEN BINDING / HIGH OXYGEN AFFINITY / Transport | ||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Lepus europaeus (European hare) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Thenmozhi, M. / Sathya Moothy, Pon. / Balasubramanian, M. / Ponnuswamy, M.N. | ||||||
Citation | Journal: To be published Title: Crystal structure determination of Lepus europaeus 2.8 A resolution Authors: Sathya Moothy, Pon. / Thenmozhi, M. / Balasubramanian, M. / Ponnuswamy, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lqd.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lqd.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 3lqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/3lqd ftp://data.pdbj.org/pub/pdb/validation_reports/lq/3lqd | HTTPS FTP |
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-Related structure data
Related structure data | 2raoS S: Starting model for refinement |
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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: 15453.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lepus europaeus (European hare) / Tissue: Red Blood CellsRed blood cell / References: UniProt: F2Z285*PLUS #2: Protein | Mass: 15955.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lepus europaeus (European hare) / Tissue: Red Blood CellsRed blood cell / References: UniProt: P08535 #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-OXY / Sequence details | A SEQUENCE DATABASE REFERENCE FOR THE CHAINS A AND C DOES NOT CURRENTLY EXIST. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 45 % PEG 3350, 50mM Tris-Hcl buffer, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 13388 / % possible obs: 90.1 % / Observed criterion σ(I): 3.6 / Redundancy: 2.73 % / Rmerge(I) obs: 0.1414 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.72 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 0.9 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RAO Resolution: 2.8→29.35 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.855 / SU B: 15.137 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.525 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.672 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→29.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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