[English] 日本語
Yorodumi- PDB-2jiy: PHOTOSYNTHETIC REACTION CENTER MUTANT WITH ALA M149 REPLACED WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jiy | ||||||
---|---|---|---|---|---|---|---|
Title | PHOTOSYNTHETIC REACTION CENTER MUTANT WITH ALA M149 REPLACED WITH TRP (CHAIN M, AM149W) | ||||||
Components | (REACTION CENTER PROTEIN ...) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / MEMBRANE PROTEIN / ELECTRON TRANSPORT / BACTERIOCHLOROPHYLL / CHLOROPHYLL / METAL-BINDING / TRANSPORT / CHROMOPHORE | ||||||
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: 2.2 Å | ||||||
Authors | Fyfe, P.K. / Potter, J.A. / Cheng, J. / Williams, C.M. / Watson, A.J. / Jones, M.R. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structural Responses to Cavity-Creating Mutations in an Integral Membrane Protein. Authors: Fyfe, P.K. / Potter, J.A. / Cheng, J. / Williams, C.M. / Watson, A.J. / Jones, M.R. #1: Journal: Photosyn. Res. / Year: 2005 Title: On the Role of Basic Residues in Adapting the Purple Bacterial Reaction Centre-Lh1 Photosystem for Growth at Elevated Temperature Authors: Watson, A.J. / Hughes, A.V. / Fyfe, P.K. / Wakeham, M.C. / Holden-Dye, K. / Heathcote, P. / Jones, M.R. #2: 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. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2jiy.cif.gz | 211.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2jiy.ent.gz | 163.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jiy_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2jiy_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 2jiy_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 2jiy_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2jiy ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2jiy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): AM149W / References: UniProt: P0C0Y7 |
---|---|
#2: Protein | Mass: 31346.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): AM149W / References: UniProt: P0C0Y8 |
#3: Protein | Mass: 34644.867 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): AM149W / References: UniProt: P0C0Y9 |
-Non-polymers , 11 types, 398 molecules
#4: Chemical | #5: Chemical | ChemComp-BCL / #6: Chemical | ChemComp-BPH / | #7: Chemical | #8: Chemical | ChemComp-CDL / | #9: Chemical | ChemComp-FE / | #10: Chemical | ChemComp-PO4 / | #11: Chemical | ChemComp-SPN / | #12: Chemical | ChemComp-CL / | #13: Chemical | ChemComp-D12 / | #14: Water | ChemComp-HOH / | |
---|
-Details
Compound details | ENGINEERED |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.5 Å3/Da / Density % sol: 76 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.977 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15.9 Å / Num. obs: 106556 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.7 / % possible all: 98.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WILD-TYPE RHODOBACTER SPHAEROIDES COORDINATES UNPUBLISHED DATA Resolution: 2.2→15.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.663 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.95 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|