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Yorodumi- PDB-1mps: PHOTOSYNTHETIC REACTION CENTER MUTANT WITH PHE M 197 REPLACED WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mps | ||||||
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Title | PHOTOSYNTHETIC REACTION CENTER MUTANT WITH PHE M 197 REPLACED WITH ARG AND TYR M 177 REPLACED WITH PHE (CHAIN M, Y177F, F197R) | ||||||
Components | (PHOTOSYNTHETIC REACTION ...) x 3 | ||||||
Keywords | PHOTOSYNTHETIC REACTION CENTER / TRANSMEMBRANE / ELECTRON TRANSPORT / PHOTOSYNTHESIS | ||||||
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: 2.55 Å | ||||||
Authors | Mcauley-Hecht, K.E. / Fyfe, P.K. / Ridge, J.P. / Prince, S. / Hunter, C.N. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R. | ||||||
Citation | 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-Hecht, K.E. / Fyfe, P.K. / Ridge, J.P. / Prince, S.M. / Hunter, C.N. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R. #1: Journal: Biochemistry / Year: 1992 Title: Construction and Characterization of a Mutant of Rhodobacter Sphaeroides with the Reaction Center as the Sole Pigment-Protein Complex Authors: Jones, M.R. / Visschers, R.W. / Van Grondelle, R. / Hunter, C.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mps.cif.gz | 198.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mps.ent.gz | 154 KB | Display | PDB format |
PDBx/mmJSON format | 1mps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/1mps ftp://data.pdbj.org/pub/pdb/validation_reports/mp/1mps | HTTPS FTP |
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-Related structure data
Related structure data | 1pcrS 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
-PHOTOSYNTHETIC REACTION ... , 3 types, 3 molecules LMH
#1: Protein | Mass: 31346.389 Da / Num. of mol.: 1 / Mutation: CHAIN M, Y177F, F197R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Cellular location (production host): CYTOPLASMIC MEMBRANE / Gene (production host): PUFQLMX / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): FM197R/YM177F / References: UniProt: P02954, UniProt: P0C0Y8*PLUS |
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#2: Protein | Mass: 34392.562 Da / Num. of mol.: 1 / Mutation: CHAIN M, Y177F, F197R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Cellular location (production host): CYTOPLASMIC MEMBRANE / Gene (production host): PUFQLMX / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): FM197R/YM177F / References: UniProt: P02953, UniProt: P0C0Y9*PLUS |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 / Mutation: CHAIN M, Y177F, F197R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Cellular location (production host): CYTOPLASMIC MEMBRANE / Gene (production host): PUFQLMX / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): FM197R/YM177F / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
-Non-polymers , 8 types, 114 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-FE2 / | #8: Chemical | ChemComp-PO4 / | #9: Chemical | ChemComp-SPN / | #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 5.2 Å3/Da / Density % sol: 76 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 7.5 / 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: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→11 Å / Num. obs: 54163 / % possible obs: 77 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / % possible all: 83 |
Reflection shell | *PLUS % possible obs: 83 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PCR Resolution: 2.55→11 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 40 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.64 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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