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Yorodumi- PDB-2x9j: Structure of the Mutant D206N of Phycoerythrobilin Synthase PebS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x9j | ||||||
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Title | Structure of the Mutant D206N of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in complex with bound substrate Biliverdin IXA | ||||||
Components | PHYCOERYTHROBILIN SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information phycoerythrobilin synthase / phytochromobilin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding Similarity search - Function | ||||||
Biological species | PROCHLOROCOCCUS PHAGE P-SSM2 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Busch, A.W.U. / Frankenberg-Dinkel, N. / Hofmann, E. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Radical Mechanism of Cyanophage Phycoerythrobilin Synthase (Pebs). Authors: Busch, A.W.U. / Reijerse, E.J. / Lubitz, W. / Hofmann, E. / Frankenberg-Dinkel, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x9j.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x9j.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 2x9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/2x9j ftp://data.pdbj.org/pub/pdb/validation_reports/x9/2x9j | HTTPS FTP |
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-Related structure data
Related structure data | 2x9iC 2vgrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper: (Code: given Matrix: (-0.990974, -0.134053, -0.000499), Vector: |
-Components
#1: Protein | Mass: 27291.855 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PROCHLOROCOCCUS PHAGE P-SSM2 (virus) / Description: CYANOPHAGE / Plasmid: PGEX-6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58MU6, phycoerythrobilin synthase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Details: 170MM (NH4)2SO4, 20%PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 2, 2008 / Details: MIRROR |
Radiation | Monochromator: SILICON 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→49 Å / Num. obs: 44404 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.88 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 5.93 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.26 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VGR Resolution: 1.85→39.687 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 20.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.26 Å2 / ksol: 0.335 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.85→39.687 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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