- PDB-2j96: The E-configuration of alfa-Phycoerythrocyanin -
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Basic information
Entry
Database: PDB / ID: 2j96
Title
The E-configuration of alfa-Phycoerythrocyanin
Components
PHYCOERYTHROCYANIN ALPHA CHAIN
Keywords
PHOTOSYNTHESIS / ELECTRON TRANSPORT / Z- TO E-ISOMERIZATION / TRANSPORT / CHROMOPHORE / BILE PIGMENT / PHYCOBILISOME / LIGHT HARVESTING / PHYCOBILIPROTEINS
Mass: 17581.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: PHYCOVIOLOBILIN CHROMOPHORE ATTACHED TO CYS84 AND REFINED AS A WHOLE Source: (natural) MASTIGOCLADUS LAMINOSUS (bacteria) / References: UniProt: P00309
#2: Chemical
ChemComp-PVN / PHYCOVIOLOBILIN / Phycoviolobilin, bound form
Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6
Resolution: 2.25→50 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE PVN CHROMOPHORE HAS BEEN ATTACHED TO CYS84 USING RESTRAINTS DERIVED FROM METHIONINE AND REFINED AS IF IT WOULD BE AN AMINO ACID
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.3086
898
4.5 %
RANDOM
Rwork
0.235
-
-
-
obs
0.235
17895
91.9 %
-
Solvent computation
Bsol: 21.1171 Å2 / ksol: 0.300406 e/Å3
Displacement parameters
Biso mean: 35.3 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.815 Å2
0 Å2
1.749 Å2
2-
-
-18.144 Å2
0 Å2
3-
-
-
12.329 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.43 Å
0.29 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.31 Å
0.21 Å
Refinement step
Cycle: LAST / Resolution: 2.25→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2478
0
86
326
2890
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
c_bond_d
0.01483
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.68283
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
21
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
2.14
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
1.58
1.5
X-RAY DIFFRACTION
c_mcangle_it
2.67
2
X-RAY DIFFRACTION
c_scbond_it
2.01
2
X-RAY DIFFRACTION
c_scangle_it
2.95
2.5
LS refinement shell
Resolution: 2.25→2.33 Å / Total num. of bins used: 10
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