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Yorodumi- PDB-1gka: The molecular basis of the coloration mechanism in lobster shell.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gka | ||||||
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Title | The molecular basis of the coloration mechanism in lobster shell. beta-crustacyanin at 3.2 A resolution | ||||||
Components | (CRUSTACYANIN ...) x 2 | ||||||
Keywords | LIPOCALIN / CRUSTACYANIN / LOBSTER / ASTAXANTHIN / BATHOCHROMIC / COLORATION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | HOMARUS GAMMARUS (European lobster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å | ||||||
Authors | Cianci, M. / Rizkallah, P.J. / Olczak, A. / Raftery, J. / Chayen, N.E. / Zagalsky, P.F. / Helliwell, J.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: The Molecular Basis of the Coloration Mechanism in Lobster Shell: Beta -Crustacyanin at 3.2-A Resolution Authors: Cianci, M. / Rizkallah, P. / Olczak, A. / Raftery, J. / Chayen, N. / Zagalsky, P. / Helliwell, J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. REMARK 900 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gka.cif.gz | 90.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gka.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gka ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gka | HTTPS FTP |
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-Related structure data
Related structure data | 1h91S 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
-CRUSTACYANIN ... , 2 types, 2 molecules AB
#1: Protein | Mass: 20558.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMARUS GAMMARUS (European lobster) / Tissue: CARAPACE / References: UniProt: P58989*PLUS |
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#2: Protein | Mass: 19688.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMARUS GAMMARUS (European lobster) / Tissue: CARAPACE / References: UniProt: P80007 |
-Non-polymers , 5 types, 35 molecules
#3: Chemical | #4: Chemical | ChemComp-D12 / | #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-EPE / | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | THIS BETA CRUSTACYANIN IS RESPONSIBLE FOR BINDING THE CAROTENOID ASTAXANTHIN THAT PROVIDES THE ...THIS BETA CRUSTACYAN |
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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: 7.3 Å3/Da / Density % sol: 78.89 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.7 / Details: pH 7.70 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Date: Nov 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 3→100 Å / Num. obs: 24504 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 3.23→3.38 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 100 Å / Num. measured all: 171943 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H91 Resolution: 3.23→100 Å / σ(F): 0
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.23→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.23→3.35 Å / Total num. of bins used: 10
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Refinement | *PLUS Lowest resolution: 100 Å / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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