+Open data
-Basic information
Entry | Database: PDB / ID: 1eyx | ||||||
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Title | CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS | ||||||
Components | (R-PHYCOERYTHRIN) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / R-PHYCOERYTHRIN / MACROSEEDING / TWIN / PROTEIN STRUCTURE / SEQUENCES / PHYCOBILIPROTEIN / RED ALGAE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Gracilaria chilensis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Contreras-Martel, C. / Legrand, P. / Piras, C. / Vernede, X. / Martinez-Oyanedel, J. / Bunster, M. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning. Authors: Contreras-Martel, C. / Martinez-Oyanedel, J. / Bunster, M. / Legrand, P. / Piras, C. / Vernede, X. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eyx.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eyx.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 1eyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/1eyx ftp://data.pdbj.org/pub/pdb/validation_reports/ey/1eyx | HTTPS FTP |
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-Related structure data
Related structure data | 1liaS 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules AKBL
#1: Protein | Mass: 17770.857 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) Gracilaria chilensis (eukaryote) / Organelle: CHLOROPLAST / References: UniProt: Q7SIG0 #2: Protein | Mass: 18634.182 Da / Num. of mol.: 2 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) Gracilaria chilensis (eukaryote) / Organelle: CHLOROPLAST / References: UniProt: Q7SIF9 |
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-Protein/peptide , 1 types, 2 molecules GH
#3: Protein/peptide | Mass: 606.694 Da / Num. of mol.: 2 / Fragment: GAMMA CHAIN / Source method: isolated from a natural source / Source: (natural) Gracilaria chilensis (eukaryote) / Organelle: CHLOROPLAST |
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-Non-polymers , 5 types, 122 molecules
#4: Chemical | #5: Chemical | ChemComp-BLA / | #6: Chemical | ChemComp-CYC / #7: Chemical | #8: Water | ChemComp-HOH / | |
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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: 1.88 Å3/Da / Density % sol: 34.7 % Description: A PERFECT HEMIHEDRAL TWINNED CRYSTAL. STANLEY DISTRIBUTION, 1.44. TWIN FRACTION, 0.48. | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 200 MM HEPES, 500 MM SODIUM CHLORIDE, 50 MM POTASIUM CHLORIDE, 15 MM SODIUM AZIDE, 16% AMMONIUM SULPHATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K | ||||||||||||||||||||||||||||||
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: ESRF / Beamline: BM14 / Wavelength: 0.9783 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 31, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9783 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→42.55 Å / Num. obs: 38751 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.16→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.039 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.039 / % possible all: 89.4 |
Reflection | *PLUS Num. measured all: 123143 |
Reflection shell | *PLUS % possible obs: 89.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LIA Resolution: 2.25→999 Å / Num. parameters: 2290 / Num. restraintsaints: 3005 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5654 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→999 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.18 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |