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Yorodumi- PDB-7ssf: Light harvesting phycobiliprotein HaPE560 from the cryptophyte He... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ssf | ||||||||||||
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Title | Light harvesting phycobiliprotein HaPE560 from the cryptophyte Hemiselmis andersenii CCMP644 | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / phycobiliprotein / antenna / light harvesting / cryptophyte / algae / globin / CALM / CaRSP / phycoerythrin / Hemiselmis | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Hemiselmis andersenii (eukaryote) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||||||||
Authors | Rathbone, H.W. / Michie, K.A. / Laos, A.L. / Curmi, P.M.G. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: Commun Biol / Year: 2023 Title: Molecular dissection of the soluble photosynthetic antenna from the cryptophyte alga Hemiselmis andersenii Authors: Rathbone, H.W. / Curmi, P.M.G. / Michie, K.A. / Green, B.R. / Laos, A.L. / Thordarson, P. / Iranmanesh, H. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: J Synchrotron Radiat / Year: 2015 Title: MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron. Authors: Cowieson, N.P. / Aragao, D. / Clift, M. / Ericsson, D.J. / Gee, C. / Harrop, S.J. / Mudie, N. / Panjikar, S. / Price, J.R. / Riboldi-Tunnicliffe, A. / Williamson, R. / Caradoc-Davies, T. #3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2004 Title: Coot: model-building tools for molecular graphics. Authors: Emsley, P. / Cowtan, K. #4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2011 Title: Overview of the CCP4 suite and current developments. Authors: Winn, M.D. / Ballard, C.C. / Cowtan, K.D. / Dodson, E.J. / Emsley, P. / Evans, P.R. / Keegan, R.M. / Krissinel, E.B. / Leslie, A.G. / McCoy, A. / McNicholas, S.J. / Murshudov, G.N. / Pannu, ...Authors: Winn, M.D. / Ballard, C.C. / Cowtan, K.D. / Dodson, E.J. / Emsley, P. / Evans, P.R. / Keegan, R.M. / Krissinel, E.B. / Leslie, A.G. / McCoy, A. / McNicholas, S.J. / Murshudov, G.N. / Pannu, N.S. / Potterton, E.A. / Powell, H.R. / Read, R.J. / Vagin, A. / Wilson, K.S. #5: Journal: J Appl Crystallogr / Year: 2007 Title: Phaser crystallographic software. Authors: McCoy, A.J. / Grosse-Kunstleve, R.W. / Adams, P.D. / Winn, M.D. / Storoni, L.C. / Read, R.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ssf.cif.gz | 650 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ssf.ent.gz | 538.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ssf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ssf_validation.pdf.gz | 6.1 MB | Display | wwPDB validaton report |
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Full document | 7ssf_full_validation.pdf.gz | 6.1 MB | Display | |
Data in XML | 7ssf_validation.xml.gz | 60.4 KB | Display | |
Data in CIF | 7ssf_validation.cif.gz | 78.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/7ssf ftp://data.pdbj.org/pub/pdb/validation_reports/ss/7ssf | HTTPS FTP |
-Related structure data
Related structure data | 4lmxS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 7713.771 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / Strain: CCMP644 #2: Protein | Mass: 18406.949 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / References: UniProt: U5T8W0 |
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-Non-polymers , 5 types, 833 molecules
#3: Chemical | ChemComp-PEB / #4: Chemical | ChemComp-AX9 / #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.53 Å3/Da / Density % sol: 51.34 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: TRIS HCl 0.162 M + PEGMME 5000 21.4 % (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→28.94 Å / Num. obs: 181639 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 14.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.424 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8893 / CC1/2: 0.546 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LMX Resolution: 1.45→28.94 Å / SU ML: 0.1588 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0252 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→28.94 Å
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Refine LS restraints |
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LS refinement shell |
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