+Open data
-Basic information
Entry | Database: PDB / ID: 6l8s | ||||||
---|---|---|---|---|---|---|---|
Title | High resolution crystal structure of crustacean hemocyanin. | ||||||
Components | (Hemocyanin) x 3 | ||||||
Keywords | OXYGEN TRANSPORT / Copper protein / Hemocyanin / Phenoloxidase / Crustacean / Arthropod | ||||||
Function / homology | Function and homology information Hemocyanin, C-terminal domain / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Panulirus japonicus (Japanese spiny lobster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Masuda, T. / Mikami, B. / Baba, S. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2020 Title: The high-resolution crystal structure of lobster hemocyanin shows its enzymatic capability as a phenoloxidase. Authors: Masuda, T. / Baba, S. / Matsuo, K. / Ito, S. / Mikami, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6l8s.cif.gz | 888.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6l8s.ent.gz | 729.7 KB | Display | PDB format |
PDBx/mmJSON format | 6l8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l8s_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6l8s_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 6l8s_validation.xml.gz | 81.8 KB | Display | |
Data in CIF | 6l8s_validation.cif.gz | 121.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/6l8s ftp://data.pdbj.org/pub/pdb/validation_reports/l8/6l8s | HTTPS FTP |
-Related structure data
Related structure data | 1hcyS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 74643.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB LC505511 Source: (natural) Panulirus japonicus (Japanese spiny lobster) |
---|---|
#2: Protein | Mass: 74611.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB LC505511 Source: (natural) Panulirus japonicus (Japanese spiny lobster) |
#3: Protein | Mass: 74565.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB LC505511 Source: (natural) Panulirus japonicus (Japanese spiny lobster) |
-Sugars , 1 types, 2 molecules
#5: Sugar |
---|
-Non-polymers , 7 types, 1371 molecules
#4: Chemical | ChemComp-CU / #6: Chemical | ChemComp-O / #7: Chemical | #8: Chemical | ChemComp-MG / #9: Chemical | ChemComp-EDO / #10: Chemical | ChemComp-CL / | #11: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.6 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Lithium sulfate monohydrate, Sodium citrate tribasic dihydrate, PEG1,000, magnesium chloride, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→42.695 Å / Num. obs: 615236 / % possible obs: 99.7 % / Redundancy: 3.78 % / Biso Wilson estimate: 21.86 Å2 / CC1/2: 0.754 / Net I/σ(I): 15.24 |
Reflection shell | Resolution: 1.58→1.68 Å / Rmerge(I) obs: 0.464 / Num. unique obs: 99005 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HCY Resolution: 1.58→42.695 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 18.77
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.59 Å2 / Biso mean: 28.8303 Å2 / Biso min: 12.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→42.695 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|