[English] 日本語
Yorodumi- PDB-1qgw: CRYSTAL STRUCTURE OF PHYCOERYTHRIN 545 FROM THE MARINE CRYPTOPHYT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qgw | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF PHYCOERYTHRIN 545 FROM THE MARINE CRYPTOPHYTE RHODOMONAS CS24 | ||||||
Components |
| ||||||
Keywords | PHOTOSYNTHESIS / PHYCOERYTHRIN / LIGHT-HARVESTING PROTEIN / CRYPTOPHYTE / PHYCOBILIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodomonas sp. CS24 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Harrop, S.J. / Wilk, K.E. / Hiller, R.G. / Curmi, P.M.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Evolution of a light-harvesting protein by addition of new subunits and rearrangement of conserved elements: crystal structure of a cryptophyte phycoerythrin at 1.63-A resolution. Authors: Wilk, K.E. / Harrop, S.J. / Jankova, L. / Edler, D. / Keenan, G. / Sharples, F. / Hiller, R.G. / Curmi, P.M. #1: Journal: J.Biol.Chem. / Year: 1992 Title: Phycobilins of Cryptophycean Algae. Occurance of Dihydrobiliverdin and Mesobiliverdin in Cryptomonad Biliproteins. Authors: Wedemayer, G.J. / Kidd, D.G. / Wemmer, D.E. / Glazer, A.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qgw.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qgw.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qgw_validation.pdf.gz | 1012.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1qgw_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1qgw_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 1qgw_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/1qgw ftp://data.pdbj.org/pub/pdb/validation_reports/qg/1qgw | HTTPS FTP |
-Related structure data
Related structure data | 1liaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
-PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA- ... , 2 types, 2 molecules AB
#1: Protein | Mass: 8135.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CSIRO DIVISION OF FISHERIES HOBART TASMAINIA AUSTRALIA Source: (natural) Rhodomonas sp. CS24 (eukaryote) / Cellular location: THYLAKOID LUMEN / Strain: CS 24 / References: UniProt: Q00433 |
---|---|
#2: Protein | Mass: 7042.138 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CSIRO DIVISION OF FISHERIES HOBART TASMAINIA AUSTRALIA Source: (natural) Rhodomonas sp. CS24 (eukaryote) / Cellular location: THYLAKOID LUMEN / Strain: CS 24 / References: UniProt: Q00433, UniProt: P30943*PLUS |
-Protein , 1 types, 2 molecules CD
#3: Protein | Mass: 18539.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CSIRO DIVISION OF FISHERIES HOBART TASMAINIA AUSTRALIA Source: (natural) Rhodomonas sp. CS24 (eukaryote) / Cellular location: THYLAKOID LUMEN / Strain: CS 24 / References: UniProt: P27198 |
---|
-Non-polymers , 5 types, 856 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-PEB / #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.86 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 1, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→30 Å / Num. obs: 264395 / % possible obs: 95.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.63→1.67 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 12 / Rsym value: 0.104 / % possible all: 79.4 |
Reflection | *PLUS Num. obs: 56582 / Num. measured all: 264395 |
Reflection shell | *PLUS % possible obs: 79.4 % / Mean I/σ(I) obs: 12 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BETA CHAIN FROM PDB ENTRY 1LIA Resolution: 1.63→20 Å / SU B: 1.506 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.149 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 8.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|