+Open data
-Basic information
Entry | Database: PDB / ID: 2bhw | |||||||||
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Title | PEA LIGHT-HARVESTING COMPLEX II AT 2.5 ANGSTROM RESOLUTION | |||||||||
Components | CHLOROPHYLL A-B BINDING PROTEIN AB80 | |||||||||
Keywords | PHOTOSYNTHESIS / LHC-II / LIGHT-HARVESTING / MEMBRANE PROTEIN / CHLOROPHYLL / CHLOROPLAST / CHROMOPHORE / MEMBRANE / PHOSPHORYLATION / PHOTOSYSTEM I / PHOTOSYSTEM II / PLASTID / THYLAKOID / TRANSIT PEPTIDE / TRANSMEMBRANE | |||||||||
Function / homology | Function and homology information plastoglobule / photosynthesis, light harvesting in photosystem I / chloroplast envelope / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / metal ion binding Similarity search - Function | |||||||||
Biological species | PISUM SATIVUM (garden pea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Standfuss, J. / Terwisscha van Scheltinga, A.C. / Lamborghini, M. / Kuehlbrandt, W. | |||||||||
Citation | Journal: Embo J. / Year: 2005 Title: Mechanisms of Photoprotection and Nonphotochemical Quenching in Pea Light-Harvesting Complex at 2.5 A Resolution. Authors: Standfuss, J. / Terwisscha Van Scheltinga, A.C. / Lamborghini, M. / Kuehlbrandt, W. #1: Journal: Nature / Year: 1994 Title: Atomic Model of Plant Light-Harvesting Complex by Electron Crystallography Authors: Kuehlbrandt, W. / Wang, D.N. / Fujiyoshi, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bhw.cif.gz | 232.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bhw.ent.gz | 198.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bhw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bhw_validation.pdf.gz | 16.5 MB | Display | wwPDB validaton report |
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Full document | 2bhw_full_validation.pdf.gz | 16.5 MB | Display | |
Data in XML | 2bhw_validation.xml.gz | 76.2 KB | Display | |
Data in CIF | 2bhw_validation.cif.gz | 85.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/2bhw ftp://data.pdbj.org/pub/pdb/validation_reports/bh/2bhw | 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein / Sugars , 2 types, 6 molecules ABC
#1: Protein | Mass: 24920.049 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / Organ: CHLOROPLAST / Tissue: LEAVES / References: UniProt: P07371 #8: Sugar | |
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-Non-polymers , 7 types, 78 molecules
#2: Chemical | ChemComp-LUX / ( #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CLA / #6: Chemical | ChemComp-CHL / #7: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Compound details | THE LIGHT-HARVESTING COMPLEX (LHC) FUNCTIONS AS A LIGHT RECEPTOR, IT CAPTURES AND DELIVERS ...THE LIGHT-HARVESTING |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 69 % Description: THE MODEL USED FOR MR WAS 3.4 ANGSTROM EM MAP. KUEHLBRANDT ET AL., 1994. |
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Crystal grow | pH: 5.5 Details: 14 % PEG 350 MMME 50 MM MES PH 5.5 10 % GLYCEROL, 20 MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 2, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 47867 / % possible obs: 85.6 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 103.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.99 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.7 / % possible all: 70.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EM MAP Resolution: 2.5→50 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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