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Yorodumi- PDB-1e14: PHOTOSYNTHETIC REACTION CENTER MUTANT WITH PHE M197 REPLACED WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+14 | ||||||
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Title | PHOTOSYNTHETIC REACTION CENTER MUTANT WITH PHE M197 REPLACED WITH ARG (CHAIN M, FM197R) AND GLY M203 REPLACED WITH ASP (CHAIN M, GM203D) | ||||||
Components | (Reaction center protein ...) x 3 | ||||||
Keywords | ELECTRON TRANSPORT / TRANSMEMBRANE / 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 / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Fyfe, P.K. / Ridge, J.P. / McAuley, K.E. / Cogdell, R.J. / Isaacs, N.W. / Jones, M.R. | ||||||
Citation | 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. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Structural Details of an Interaction between Cardiolipin and an Integral Membrane Protein Authors: Mcauley, K.E. / Fyfe, P.K. / Ridge, J.P. / Isaacs, N.W. / Cogdell, R.J. / 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. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e14.cif.gz | 205.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e14.ent.gz | 157.6 KB | Display | PDB format |
PDBx/mmJSON format | 1e14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e14_validation.pdf.gz | 957.4 KB | Display | wwPDB validaton report |
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Full document | 1e14_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1e14_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 1e14_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/1e14 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/1e14 | HTTPS FTP |
-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
-Reaction center protein ... , 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 MEMBRANE / Gene: puhA / Plasmid: PRKEH10D / Gene (production host): PUFQLMX / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): WM115F/FM197R / References: UniProt: P0C0Y7 |
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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 MEMBRANE / Gene: pufL / Plasmid: PRKEH10D / Gene (production host): PUFQLMX / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): WM115F/FM197R / References: UniProt: P0C0Y8 |
#3: Protein | Mass: 34466.598 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / Gene: pufM / Plasmid: PRKEH10D / Gene (production host): PUFQLMX / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): WM115F/FM197R / References: UniProt: P0C0Y9 |
-Non-polymers , 8 types, 126 molecules
#4: Chemical | #5: Chemical | ChemComp-BCL / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-SPN / | #10: Chemical | ChemComp-CDL / | #11: Water | ChemComp-HOH / | |
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-Details
Compound details | CHAIN M ENGINEERED |
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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: 74.5 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, sitting drop / Details: Mcauley, K.E., (1998) Biochemistry, 37, 4740. | |||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.83 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.83 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 53597 / % possible obs: 92.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.38 / % possible all: 83 |
Reflection shell | *PLUS % possible obs: 83 % / Rmerge(I) obs: 0.388 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WILD-TYPE RHODOBACTER SPHAEROIDES COORDINATES (UNPUBLISHED DATA) Resolution: 2.7→30 Å / SU B: 9.12 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.36 / ESU R Free: 0.28 Details: DISORDERED REGIONS HAVE BEEN GIVEN OCCUPANCIES OF ZERO. REGIONS: U10 502 C20 TO C41 THE MOST COMMON ACYL CHAIN LENGTH IN CARDIOLIPIN FROM RHODOBACTER SPHAEROIDES IS 18 CARBONS. THE ENDS OF ...Details: DISORDERED REGIONS HAVE BEEN GIVEN OCCUPANCIES OF ZERO. REGIONS: U10 502 C20 TO C41 THE MOST COMMON ACYL CHAIN LENGTH IN CARDIOLIPIN FROM RHODOBACTER SPHAEROIDES IS 18 CARBONS. THE ENDS OF THE ACYL CHAINS WERE NOT RESOLVED IN THE ELECTRON DENSITY AND THEREFORE THE CARDIOLIPIN SPECIES HAS NOT BEEN DETERMINED. THE ACYL CHAINS BUILT INTO THE MODEL HAVE DIFFERING LENGTHS: TWO CHAINS OF 15 CARBONS, ONE OF 14 CARBONS AND ONE OF 9 CARBONS.
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Displacement parameters | Biso mean: 42.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |