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Yorodumi- PDB-3l6w: Structure of the collar functional unit (KLH1-H) of keyhole limpe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l6w | ||||||
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Title | Structure of the collar functional unit (KLH1-H) of keyhole limpet hemocyanin | ||||||
Components | Hemocyanin 1 | ||||||
Keywords | OXYGEN BINDING / HEMOCYANIN / CUPREDOXIN DOMAIN / COPPER-BINDING PROTEIN / METAL-BINDING | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Megathura crenulata (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Jaenicke, E. / Buechler, K. / Markl, J. / Decker, H. / Barends, T.R.M. | ||||||
Citation | Journal: Biochem.J. / Year: 2009 Title: The Cupredoxin-like Domains in Hemocyanins. Authors: Jaenicke, E. / Buchler, K. / Markl, J. / Decker, H. / Barends, T.R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l6w.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l6w.ent.gz | 21.9 KB | Display | PDB format |
PDBx/mmJSON format | 3l6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l6w_validation.pdf.gz | 348.6 KB | Display | wwPDB validaton report |
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Full document | 3l6w_full_validation.pdf.gz | 348.5 KB | Display | |
Data in XML | 3l6w_validation.xml.gz | 1.5 KB | Display | |
Data in CIF | 3l6w_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/3l6w ftp://data.pdbj.org/pub/pdb/validation_reports/l6/3l6w | HTTPS FTP |
-Related structure data
Related structure data | 1js8S 3eu2 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: 56623.797 Da / Num. of mol.: 2 / Fragment: collar subunit / Source method: isolated from a natural source / Source: (natural) Megathura crenulata (invertebrata) / References: UniProt: Q53IP9, UniProt: Q10583*PLUS |
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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: 5.82 Å3/Da / Density % sol: 78.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 9% PEG 1000, 50mM phosphate/citrate buffer, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97941 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2006 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97941 Å / Relative weight: 1 |
Reflection | Resolution: 4→30 Å / Num. obs: 22294 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 4→4.2 Å / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 3.46 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JS8 Highest resolution: 4 Å Details: THE COORDINATES CONTAIN ONLY A CA TRACE. NO REFINEMENT WAS CARRIED OUT | ||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4 Å
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