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Yorodumi- PDB-1kzu: INTEGRAL MEMBRANE PERIPHERAL LIGHT HARVESTING COMPLEX FROM RHODOP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kzu | |||||||||
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Title | INTEGRAL MEMBRANE PERIPHERAL LIGHT HARVESTING COMPLEX FROM RHODOPSEUDOMONAS ACIDOPHILA STRAIN 10050 | |||||||||
Components | (LIGHT HARVESTING PROTEIN B-800/850) x 2 | |||||||||
Keywords | LIGHT-HARVESTING PROTEIN / ANTENNA COMPLEX / LH2 COMPLEX / BACTERIOCHLOROPHYLL / PURPLE BACTERIA | |||||||||
Function / homology | Function and homology information organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rhodoblastus acidophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å | |||||||||
Authors | Cogdell, R.J. / Freer, A.A. / Isaacs, N.W. / Hawthornthwaite-Lawless, A.M. / Mcdermott, G. / Papiz, M.Z. / Prince, S.M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Apoprotein structure in the LH2 complex from Rhodopseudomonas acidophila strain 10050: modular assembly and protein pigment interactions. Authors: Prince, S.M. / Papiz, M.Z. / Freer, A.A. / McDermott, G. / Hawthornthwaite-Lawless, A.M. / Cogdell, R.J. / Isaacs, N.W. #1: Journal: Photochem.Photobiol. / Year: 1996 Title: Structure-Based Calculations on the Optical Spectra of the Lh2 Bacteriochlorophyll-Protein Complex from Rhodopseudomonas Acidophila Authors: Sauer, K. / Cogdell, R.J. / Prince, S.M. / Freer, A. / Isaacs, N.W. / Scheer, H. #2: Journal: Structure / Year: 1996 Title: Pigment-Pigment Interactions and Energy Transfer in the Antenna Complex of the Photosynthetic Bacterium Rhodopseudomonas Acidophila Authors: Freer, A. / Prince, S. / Sauer, K. / Papiz, M. / Hawthornthwaite-Lawless, A. / Mcdermott, G. / Cogdell, R. / Isaacs, N.W. #3: Journal: Trends Plant Sci. / Year: 1996 Title: A Model for the Photosynthetic Apparatus of Purple Bacteria Authors: Papiz, M.Z. / Prince, S.M. / Hawthornthwaite-Lawless, A.M. / Mcdermott, G. / Freer, A. / Isaacs, N.W. / Cogdell, R.J. #4: Journal: Nature / Year: 1995 Title: Crystal Structure of an Integral Membrane Light-Harvesting Complex from Photosynthetic Bacteria Authors: Mcdermott, G. / Prince, S.M. / Freer, A.A. / Hawthornthwaite-Lawless, A.M. / Papiz, M.Z. / Cogdell, R.J. / Isaacs, N.W. #5: Journal: Curr.Opin.Struct.Biol. / Year: 1995 Title: Light-Harvesting Mechanisms in Purple Photosynthetic Bacteria Authors: Isaacs, N.W. / Cogdell, R.J. / Freer, A.A. / Prince, S.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kzu.cif.gz | 87.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kzu.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kzu_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 1kzu_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 1kzu_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 1kzu_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/1kzu ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kzu | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE CELL IS A HEXAGONALLY INDEXED RHOMBOHEDRAL CELL. THE DEPOSITORS PROVIDED ONE-THIRD OF THE ASYMMETRIC UNIT. THE REMAINING TWO-THIRDS WERE GENERATED BY THE PDB USING THE MTRIX TRANSFORMATIONS SO THAT THE ENTRY CONTAINS A COMPLETE ASYMMETRIC UNIT. ASSOCIATION OF CHAIN IDENTIFIERS AND HET ATOMS PROTEIN CHAIN HET AND SOLVENT CHAIN A, B C D, E F G, H I |
-Components
#1: Protein | Mass: 5686.733 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 10050 / References: UniProt: P26789 #2: Protein/peptide | Mass: 4559.203 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 10050 / References: UniProt: P26790 #3: Sugar | ChemComp-RG1 / #4: Chemical | ChemComp-BCL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 9 |
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-Sample preparation
Crystal | Density % sol: 73 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 9.5 / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→12 Å / Num. obs: 28574 / % possible obs: 98.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 57.77 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.5→12 Å / Rfactor Rfree error: 0.028 / σ(F): 2
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Displacement parameters | Biso mean: 34.52 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→12 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.085
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 27855 / Rfactor Rfree: 0.253 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.302 |