+Open data
-Basic information
Entry | Database: PDB / ID: 4yd9 | |||||||||
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Title | Crystal structure of squid hemocyanin | |||||||||
Components | (hemocyanin) x 3 | |||||||||
Keywords | OXYGEN TRANSPORT / decamer / supermolecule | |||||||||
Function / homology | CU2-O2 CLUSTER Function and homology information | |||||||||
Biological species | Todarodes pacificus (Japanese flying squid) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Matsuno, A. / Gai, Z. / Kato, K. / Tanaka, Y. / Yao, M. | |||||||||
Citation | Journal: Structure / Year: 2015 Title: Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 angstrom Resolution Authors: Gai, Z. / Matsuno, A. / Kato, K. / Kato, S. / Khan, M.R.I. / Shimizu, T. / Yoshioka, T. / Kato, Y. / Kishimura, H. / Kanno, G. / Miyabe, Y. / Terada, T. / Tanaka, Y. / Yao, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yd9.cif.gz | 6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4yd9.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4yd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yd9_validation.pdf.gz | 13.7 MB | Display | wwPDB validaton report |
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Full document | 4yd9_full_validation.pdf.gz | 15.1 MB | Display | |
Data in XML | 4yd9_validation.xml.gz | 1.2 MB | Display | |
Data in CIF | 4yd9_validation.cif.gz | 1.6 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/4yd9 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/4yd9 | HTTPS FTP |
-Related structure data
Related structure data | 3j32S 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
-Protein , 3 types, 30 molecules ADGJMPSVYbBEHKNQTWZcCFILORUXad
#1: Protein | Mass: 228841.391 Da / Num. of mol.: 10 / Fragment: N-terminal residues 1-2000 / Source method: isolated from a natural source Source: (natural) Todarodes pacificus (Japanese flying squid) #2: Protein | Mass: 105798.141 Da / Num. of mol.: 10 / Fragment: residues 2001-2920 / Source method: isolated from a natural source Source: (natural) Todarodes pacificus (Japanese flying squid) #3: Protein | Mass: 45062.883 Da / Num. of mol.: 10 / Fragment: C-terminal residues 2921-3314 / Source method: isolated from a natural source Source: (natural) Todarodes pacificus (Japanese flying squid) |
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-Sugars , 5 types, 50 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 1 types, 80 molecules
#9: Chemical | ChemComp-CUO / |
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-Details
Sequence details | THREE ENTITIES IN THIS STRUCTURE ARE FRAGMENTS OF THE ENTIRE PROTEIN. HOWEVER, THE TRACE AMONG ...THREE ENTITIES IN THIS STRUCTURE ARE FRAGMENTS OF THE ENTIRE PROTEIN. HOWEVER, THE TRACE AMONG FRAGMENTS WERE NOT IDENTIFIED |
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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: 3.79 Å3/Da / Density % sol: 67.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, HEPES, CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.1 Å / Num. obs: 1072359 / % possible obs: 98.9 % / Redundancy: 2.56 % / Rsym value: 0.113 / Net I/σ(I): 7.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3j32 Resolution: 3→49.099 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.099 Å
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Refine LS restraints |
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LS refinement shell |
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