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Yorodumi- PDB-1e6d: PHOTOSYNTHETIC REACTION CENTER MUTANT WITH TRP M115 REPLACED WITH... -
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-Basic information
Entry | Database: PDB / ID: 1e6d | ||||||
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Title | PHOTOSYNTHETIC REACTION CENTER MUTANT WITH TRP M115 REPLACED WITH PHE (CHAIN M, WM115F) PHE M197 REPLACED WITH ARG (CHAIN M, FM197R) | ||||||
Components | (PHOTOSYNTHETIC REACTION CENTER ...Photosynthetic reaction centre) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / TRANSMEMBRANE / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / membrane => GO:0016020 / metal ion binding Similarity search - Function | ||||||
Biological species | RHODOBACTER SPHAEROIDES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ridge, J.P. / Fyfe, P.K. / McAuley, K.E. / Van Brederode, M.E. / Robert, B. / Van Grondelle, R. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R. | ||||||
Citation | Journal: Biochem.J. / Year: 2000 Title: An Examination of How Structural Changes Can Affect the Rate of Electron Transfer in a Mutated Bacterial Photoreaction Centre Authors: Ridge, J.P. / Fyfe, P.K. / Mcauley, K.E. / Van Brederode, M.E. / Robert, B. / Van Grondelle, R. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R. #1: Journal: Biochemistry / Year: 2000 Title: Structural Consequences of the Replacement of Glycine M203 with Aspartic Acid in the Reaction Center from Rhodobacter Sphaeroides Authors: Fyfe, P.K. / Ridge, J.P. / Mcauley, K.E. / Cogdell, R.J. / Isaacs, N.W. / Jones, M.R. #2: Journal: Biochemistry / Year: 1998 Title: Structural Studies of Wild-Type and Mutant Reaction Centers from an Antenna-Deficient Strain of Rhodobacter Sphaeroides: Monitoring the Optical Properties of the Complex from Bacterial Cell to Crystal Authors: Mcauley, K.E. / Fyfe, P.K. / Ridge, J.P. / Prince, S.M. / Hunter, C.N. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R. #3: Journal: Photosyn. Res. / Year: 1998 Title: Crystallographic Studies of Mutant Reaction Centers from Rhodobacter Sphaeroides Authors: Fyfe, P.K. / Mcauley-Hecht, K.E. / Ridge, J.P. / Prince, S.M. / Fritzsch, G. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e6d.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e6d.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 1e6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/1e6d ftp://data.pdbj.org/pub/pdb/validation_reports/e6/1e6d | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
-PHOTOSYNTHETIC REACTION CENTER ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Cellular location: CYTOPLASMIC MEMBRANECell membrane / Gene: PUFQLMX / Plasmid: PRKEH10D / Gene (production host): PUFQLMX / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): WM115F/FM197R / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
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#2: Protein | Mass: 31346.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Cellular location: CYTOPLASMIC MEMBRANECell membrane / Gene: PUFQLMX / Plasmid: PRKEH10D / Gene (production host): PUFQLMX / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): WM115F/FM197R / References: UniProt: P02954, UniProt: P0C0Y8*PLUS |
#3: Protein | Mass: 34369.523 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Cellular location: CYTOPLASMIC MEMBRANECell membrane / Gene: PUFQLMX / Plasmid: PRKEH10D / Gene (production host): PUFQLMX / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): WM115F/FM197R / References: UniProt: P02953, UniProt: P0C0Y9*PLUS |
-Non-polymers , 8 types, 231 molecules
#4: Chemical | ChemComp-LDA / #5: Chemical | ChemComp-BCL / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-SPN / | #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Details
Compound details | CHAIN M ENGINEERED MUTATION TRP115PHE, PHE197ARG THE PHOTOSYNTHETIC REACTION CENTER MEDIATES THE ...CHAIN M ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
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-Sample preparation
Crystal | Density Matthews: 5.4 Å3/Da / Density % sol: 75.2 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.95 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→26.4 Å / Num. obs: 90885 / % possible obs: 94.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.53 / % possible all: 71.2 |
Reflection | *PLUS Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 71.2 % / Rmerge(I) obs: 0.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WILD-TYPE RHODOBACTER SPHAEROIDES COORDINATES (UNPUBLISHED DATA) Resolution: 2.3→26.4 Å / SU B: 4.34 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.14
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Displacement parameters | Biso mean: 38.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→26.4 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.174 / Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |