Iodine in PDB 5b34: Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla

The structure of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla, PDB code: 5b34 was solved by E.Mizohata, T.Nakane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.200, 103.000, 128.700, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 21.6

The binding sites of Iodine atom in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla (pdb code 5b34). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla, PDB code: 5b34:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:86.0 occ:0.60 I3 A:4QL302 0.0 86.0 0.6 C6 A:4QL302 2.1 87.5 0.6 C1 A:4QL302 3.0 93.0 0.6 C5 A:4QL302 3.0 74.2 0.6 N13 A:4QL302 3.1 64.4 0.6 C7 A:4QL302 3.1 94.4 0.6 O8 A:4QL302 3.1 0.3 0.6 C17 A:4QL302 3.7 73.4 0.6 CG2 A:VAL173 3.7 60.3 1.0 O9 A:4QL302 3.8 0.1 0.6 C1 A:OCT304 4.0 69.9 0.4 C23 A:HP6312 4.1 0.1 1.0 C21 A:HP6312 4.2 0.0 1.0 C18 A:4QL302 4.3 76.6 0.6 C2 A:4QL302 4.3 95.1 0.6 C4 A:4QL302 4.3 81.0 0.6 O25 A:4QL302 4.4 69.4 0.6 O A:HOH416 4.6 86.5 1.0 C2 A:OCT304 4.7 69.7 0.4 C22 A:HP6312 4.7 0.2 1.0 C3 A:4QL302 4.8 79.1 0.6 CG1 A:VAL173 4.8 67.5 1.0 O A:HOH406 4.9 80.6 1.0 CB A:VAL173 4.9 58.0 1.0 C20 A:HP6312 5.0 0.5 1.0

Iodine binding site 2 out of 6 in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:75.0 occ:0.60 I2 A:4QL302 0.0 75.0 0.6 C4 A:4QL302 2.1 81.0 0.6 C3 A:4QL302 3.0 79.1 0.6 C5 A:4QL302 3.0 74.2 0.6 C10 A:4QL302 3.1 81.0 0.6 N13 A:4QL302 3.3 64.4 0.6 C2 A:OCT304 3.4 69.7 0.4 O12 A:4QL302 3.4 77.9 0.6 O25 A:4QL302 3.5 69.4 0.6 C17 A:4QL302 3.6 73.4 0.6 O11 A:4QL302 3.7 89.3 0.6 C1 A:OCT304 3.9 69.9 0.4 ND2 A:ASN176 4.0 58.6 1.0 C2 A:4QL302 4.3 95.1 0.6 C6 A:4QL302 4.3 87.5 0.6 O A:HOH416 4.8 86.5 1.0 C3 A:OCT304 4.8 67.6 0.4 C18 A:4QL302 4.8 76.6 0.6 C1 A:4QL302 4.8 93.0 0.6

Iodine binding site 3 out of 6 in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:0.3 occ:0.60 I1 A:4QL302 0.0 0.3 0.6 C2 A:4QL302 2.1 95.1 0.6 C3 A:4QL302 3.0 79.1 0.6 C1 A:4QL302 3.1 93.0 0.6 C10 A:4QL302 3.2 81.0 0.6 C7 A:4QL302 3.3 94.4 0.6 O9 A:4QL302 3.4 0.1 0.6 O11 A:4QL302 3.5 89.3 0.6 O12 A:4QL302 3.7 77.9 0.6 O8 A:4QL302 4.1 0.3 0.6 C4 A:4QL302 4.3 81.0 0.6 C6 A:4QL302 4.3 87.5 0.6 O A:HOH406 4.7 80.6 1.0 O A:HOH416 4.7 86.5 1.0 C5 A:4QL302 4.9 74.2 0.6

Iodine binding site 4 out of 6 in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:75.2 occ:0.50 I3 A:4QL303 0.0 75.2 0.5 O25 A:4QL303 1.4 0.4 0.5 C6 A:4QL303 2.1 86.6 0.5 C17 A:4QL303 2.6 0.1 0.5 C5 A:4QL303 3.0 81.8 0.5 C1 A:4QL303 3.1 69.1 0.5 O A:ILE222 3.1 59.2 1.0 N13 A:4QL303 3.2 83.1 0.5 C7 A:4QL303 3.5 68.8 0.5 CB A:SER226 3.5 69.9 1.0 C1 A:OCT305 3.7 70.7 0.4 CA A:SER226 3.7 64.8 1.0 C18 A:4QL303 3.7 0.9 0.5 N A:SER226 3.8 64.1 1.0 O9 A:4QL303 3.8 65.8 0.5 C20 A:HP6312 4.0 0.5 1.0 C A:ARG225 4.0 64.3 1.0 C2 A:OCT305 4.0 78.2 0.4 O A:ARG225 4.1 69.2 1.0 C A:ILE222 4.1 53.6 1.0 O8 A:4QL303 4.1 65.2 0.5 C3 A:OCT305 4.3 81.0 0.4 CG2 A:ILE222 4.3 59.4 1.0 C4 A:4QL303 4.3 89.2 0.5 C2 A:4QL303 4.4 83.3 0.5 CA A:ILE222 4.4 58.6 1.0 CB A:ARG225 4.5 67.1 1.0 CA A:ARG225 4.8 60.0 1.0 OG A:SER226 4.8 66.5 1.0 C3 A:4QL303 4.9 84.1 0.5 CB A:ILE222 5.0 59.1 1.0

Iodine binding site 5 out of 6 in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:0.9 occ:0.50 I2 A:4QL303 0.0 0.9 0.5 C4 A:4QL303 2.1 89.2 0.5 C5 A:4QL303 3.0 81.8 0.5 N13 A:4QL303 3.0 83.1 0.5 C3 A:4QL303 3.1 84.1 0.5 C10 A:4QL303 3.2 91.1 0.5 O12 A:4QL303 3.5 95.6 0.5 C1 A:OCT305 3.6 70.7 0.4 O11 A:4QL303 3.8 92.0 0.5 C2 A:OCT305 3.9 78.2 0.4 C17 A:4QL303 4.3 0.1 0.5 C6 A:4QL303 4.3 86.6 0.5 C2 A:4QL303 4.3 83.3 0.5 C19 A:4QL303 4.6 96.7 0.5 C21 A:HP6312 4.8 0.0 1.0 C1 A:4QL303 4.9 69.1 0.5

Iodine binding site 6 out of 6 in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with Iodine- Labeled Detergent HAD13A Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:90.6 occ:0.50 I1 A:4QL303 0.0 90.6 0.5 C2 A:4QL303 2.1 83.3 0.5 C3 A:4QL303 3.0 84.1 0.5 C1 A:4QL303 3.0 69.1 0.5 C7 A:4QL303 3.1 68.8 0.5 C10 A:4QL303 3.2 91.1 0.5 O8 A:4QL303 3.4 65.2 0.5 O11 A:4QL303 3.5 92.0 0.5 O9 A:4QL303 3.6 65.8 0.5 O12 A:4QL303 3.8 95.6 0.5 CD A:ARG227 3.9 0.7 1.0 NE A:ARG227 4.1 0.1 1.0 OE1 A:GLU166 4.2 0.2 1.0 C4 A:4QL303 4.3 89.2 0.5 C6 A:4QL303 4.4 86.6 0.5 CZ A:ARG227 4.5 0.8 1.0 NH1 A:ARG227 4.7 0.9 1.0 C5 A:4QL303 4.9 81.8 0.5

T.Nakane, S.Hanashima, M.Suzuki, H.Saiki, T.Hayashi, K.Kakinouchi, S.Sugiyama, S.Kawatake, S.Matsuoka, N.Matsumori, E.Nango, J.Kobayashi, T.Shimamura, K.Kimura, C.Mori, N.Kunishima, M.Sugahara, Y.Takakyu, S.Inoue, T.Masuda, T.Hosaka, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, M.Yabashi, T.Inoue, O.Nureki, S.Iwata, M.Murata, E.Mizohata. Membrane Protein Structure Determination By Sad, Sir, or Siras Phasing in Serial Femtosecond Crystallography Using An Iododetergent Proc.Natl.Acad.Sci.Usa V. 113 13039 2016.
ISSN: ESSN 1091-6490
PubMed: 27799539
DOI: 10.1073/PNAS.1602531113