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Yorodumi- PDB-3pi3: Crystallographic Structure of HbII-oxy from Lucina pectinata at pH 5.0 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pi3 | ||||||
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Title | Crystallographic Structure of HbII-oxy from Lucina pectinata at pH 5.0 | ||||||
Components | Hemoglobin II | ||||||
Keywords | OXYGEN TRANSPORT / pH behavior / Oxygen Carrier | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Phacoides pectinatus (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Gavira, J.A. / Nieves-Marrero, C.A. / Ruiz-Martinez, C.R. / Estremera-Andujar, R.A. / Lopez-Garriga, J. / Garcia-Ruiz, J.M. | ||||||
Citation | Journal: To be Published Title: pH-dependence crystallographic studies of the oxygen carrier hemoglobin II from Lucina pectinata Authors: Nieves-Marrero, C.A. / Ruiz-Martinez, C.R. / Estremera-Andujar, R.A. / Lopez-Garriga, J. / Garcia-Ruiz, J.M. / Gavira, J.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Two-step counterdiffusion protocol for the crystallization of heamoglobin II from Lucina pectinata in the pH range 4-9 Authors: Nieves-Marrero, C.A. / Ruiz-Martinez, C.R. / Estremera-Andujar, R.A. / Gonzalez-Ramirez, L.A. / Lopez-Garriga, J. / Gavira, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pi3.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pi3.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pi3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3pi3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3pi3_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 3pi3_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/3pi3 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/3pi3 | HTTPS FTP |
-Related structure data
Related structure data | 3pi1C 3pi2C 3pi4C 2olpS 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 17041.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phacoides pectinatus (invertebrata) / References: UniProt: Q86G74, UniProt: P41261*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.07 Å3/Da / Density % sol: 59.99 % / Mosaicity: 0.432 ° |
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Crystal grow | Temperature: 293 K / Method: capillary counterdiffusion / pH: 5 Details: Sodium Formate, pH 5.0, Capillary Counterdiffusion, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.88506 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 6, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.88506 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→20 Å / Num. all: 31837 / Num. obs: 31837 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 28.569 Å2 / Rmerge(I) obs: 0.138 / Rsym value: 0.138 / Χ2: 1.092 / Net I/σ(I): 15.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OLP Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2368 / WRfactor Rwork: 0.1985 / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.8738 / SU R Cruickshank DPI: 0.1338 / SU Rfree: 0.1276 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.83 Å2 / Biso mean: 32.0787 Å2 / Biso min: 11.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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