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Yorodumi- PDB-4rmp: Crystal structure of allophycocyanin from marine cyanobacterium P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rmp | ||||||
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Title | Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM | ||||||
Components | (Allophycocyanin) x 2 | ||||||
Keywords | PHOTOSYNTHESIS / Phycocyanobilin chromophore / Globin-like fold (SCOP / 46457) / Light harvesting Phycobiliprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Phormidium rubidum A09DM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.506 Å | ||||||
Authors | Kumar, V. / Gupta, G.D. / Sonani, R.R. / Madamwar, D. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM. Authors: Sonani, R.R. / Gupta, G.D. / Madamwar, D. / Kumar, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rmp.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rmp.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 4rmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rmp_validation.pdf.gz | 1019.3 KB | Display | wwPDB validaton report |
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Full document | 4rmp_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4rmp_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 4rmp_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/4rmp ftp://data.pdbj.org/pub/pdb/validation_reports/rm/4rmp | HTTPS FTP |
-Related structure data
Related structure data | 1kn1S 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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Details | THE ASYMMETRIC UNIT CONTAINS ONE EACH A AND B-CHAINS WHICH FORM A HETERODIMER (KNOWN AS ALPHA/BETA MONOMER). THREE ALPHA/BETA MONOMERS FORM A BIOLOGICAL UNIT. THE HEXAMER (TRIMER of ALPHA/BETA MONOMERS) IS GENERATED BY CRYSTALLOGRAPHIC SYMMETRY |
-Components
#1: Protein | Mass: 17492.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Marine cyanobacterium isolated from rocky shores of Gujarat Source: (natural) Phormidium rubidum A09DM (bacteria) / References: UniProt: A0A078K1U6 | ||||
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#2: Protein | Mass: 17438.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Marine cyanobacterium isolated from rocky shores of Gujarat Source: (natural) Phormidium rubidum A09DM (bacteria) / References: UniProt: A0A078K4M9 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | NATURAL VARIANTS OF THE UNP REFERENCE, AS CONFIRMED BY NUCLEOTIDE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.87 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% (w/v) PEG 6000, 0.1M bicine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 17, 2014 / Details: HELIOS Cu X-RAY OPTICS |
Radiation | Monochromator: HELIOS Cu X-RAY OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.506→35 Å / Num. all: 13362 / Num. obs: 13362 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Biso Wilson estimate: 41.97 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.506→2.64 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1903 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KN1 Resolution: 2.506→29.226 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML Details: The covalent bonds between S atoms of Cys-81 and the chromophore (CYC) were restrained to a distance of 1.8A for both A and B chains
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.17 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.266 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.506→29.226 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
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