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Open data
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Basic information
Entry | Database: PDB / ID: 5aqd | ||||||
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Title | Crystal structure of Phormidium Phycoerythrin at pH 8.5 | ||||||
![]() | (PHYCOERYTHRIN ...) x 2 | ||||||
![]() | PHOTOSYNTHESIS / PHYCOBILISOME PROTEIN / PHYCOERYTHRIN ALPHA CHAIN / PHYCOERYTHRIN BETA CHAIN / PEB CHROMOPHORE / PROTEIN-CHROMOPHORE LINKAGE | ||||||
Function / homology | ![]() phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, V. / Sharma, M. / Sonani, R.R. / Gupta, G.D. / Madamwar, D. | ||||||
![]() | ![]() Title: Crystal Structure Analysis of C-Phycoerythrin from Marine Cyanobacterium Phormidium Sp. A09Dm. Authors: Kumar, V. / Sonani, R.R. / Sharma, M. / Gupta, G.D. / Madamwar, D. #1: Journal: Acta Crystallogr., Sect F / Year: 2015 Title: Phormidium Phycoerythrin Forms Hexamers in Crystals: A Crystallographic Study Authors: Sonani, R.R. / Sharma, M. / Gupta, G.D. / Kumar, V. / Madamwar, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 895.6 KB | Display | ![]() |
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PDB format | ![]() | 760.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 18.5 MB | Display | ![]() |
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Full document | ![]() | 18.1 MB | Display | |
Data in XML | ![]() | 222.3 KB | Display | |
Data in CIF | ![]() | 284 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fvbC ![]() 2vjhS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-PHYCOERYTHRIN ... , 2 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX
#1: Protein | Mass: 17660.830 Da / Num. of mol.: 12 / Fragment: ALPHA CHAIN, RESIDUES 1-164 / Source method: isolated from a natural source Details: PROTEIN-CHROMOPHORE LINK BETWEEN CYS-82 AND PEB-166 PROTEIN-CHROMOPHORE LINK BETWEEN CYS-139 AND PEB-167 Source: (natural) ![]() #2: Protein | Mass: 19370.189 Da / Num. of mol.: 12 / Fragment: BETA CHAIN, RESIDUES 1-184 / Source method: isolated from a natural source Details: PROTEIN-CHROMOPHORE LINK BETWEEN CYS-80 AND PEB-186 PROTEIN-CHROMOPHORE LINK BETWEEN CYS-165 AND PEB-187 PROTEIN-CHROMOPHORE LINK BETWEEN CYS-48 AND PEB-188 PROTEIN-CHROMOPHORE LINK BETWEEN CYS-59 AND PEB-188 Source: (natural) ![]() |
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-Non-polymers , 4 types, 3799 molecules ![](data/chem/img/PEB.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PEB / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | FOR CHAINS A TO L THE PEPTIDE SEQUENCE DEDUCED FROM GENE SEQUENCE (GENBANK CEQ38274.3) CONSISTS OF ...FOR CHAINS A TO L THE PEPTIDE SEQUENCE DEDUCED FROM GENE SEQUENCE (GENBANK CEQ38274.3) CONSISTS OF RESIDUES 1-160. THE FOUR C- TERMINAL AMINO ACIDS WERE DEDUCED FROM CRYSTAL STRUCTURE FOR CHAINS M TO X THE PEPTIDE SEQUENCE DEDUCED FROM GENE SEQUENCE (GENBANK CEQ38275.1) CONSISTS OF 8-184 AMINO ACIDS. SEVEN N- TERMINAL AMINO ACIDS WERE DEDUCED FROM CRYSTAL STRUCTURE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.3 % Description: STRUCTURE WAS SOLVED USING TRUNCATED MONOMER OF PDB ENTRY 2VJH. PROTEIN PHASES WERE ARRIVED AT USING 12-FOLD NCS-AVERAGING |
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Crystal grow | pH: 8.5 Details: PROTEIN CONCENTRATION 9.2 MG/ML. 1.25 M AMMONIUM SULPHATE, 0.075M TRSIS-HCL (PH 8.5), 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2014 |
Radiation | Monochromator: SI (111) AND SI (220) DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→29.29 Å / Num. obs: 245717 / % possible obs: 96.1 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Biso Wilson estimate: 15.67 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.12→2.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.2 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VJH Resolution: 2.121→29.291 Å / SU ML: 0.26 / σ(F): 1.96 / Phase error: 24.04 / Stereochemistry target values: ML Details: RESIDUES 21-27 OF M,N,O,P,Q,R,S,T, ,U,V,W,X CHAINS ARE DISORDERED DISORDERED REGIONS SHOW POOR ELECTRON DENISTY
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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: 17.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.121→29.291 Å
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Refine LS restraints |
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LS refinement shell |
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