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- PDB-6j55: Crystal structure of an iron superoxide dismutate (FeSOD) from a ... -

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Basic information

Entry
Database: PDB / ID: 6j55
TitleCrystal structure of an iron superoxide dismutate (FeSOD) from a pathogenic Acanthamoeba castellanii
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / iron superoxide dismutase / Acanthamoeba castellanii
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33000486301 Å
AuthorsLee, K.H. / Dao, T.O. / Asaithambi, K. / Na, B.K.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2015R1D1A1A01060694 Korea, Republic Of
National Research Foundation (Korea)NRF-2016M3D3A1A01913246 Korea, Republic Of
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of an iron superoxide dismutase from the pathogenic amoeba Acanthamoeba castellanii.
Authors: Dao, O. / Asaithambi, K. / Na, B.K. / Lee, K.H.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

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Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
E: Superoxide dismutase
F: Superoxide dismutase
G: Superoxide dismutase
H: Superoxide dismutase
I: Superoxide dismutase
J: Superoxide dismutase
K: Superoxide dismutase
L: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,11624
Polymers283,44612
Non-polymers67012
Water15,889882
1
A: Superoxide dismutase
B: Superoxide dismutase
E: Superoxide dismutase
H: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7058
Polymers94,4824
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-59 kcal/mol
Surface area31950 Å2
MethodPISA
2
C: Superoxide dismutase
D: Superoxide dismutase
F: Superoxide dismutase
G: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7058
Polymers94,4824
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-56 kcal/mol
Surface area32170 Å2
MethodPISA
3
I: Superoxide dismutase
J: Superoxide dismutase
K: Superoxide dismutase
L: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7058
Polymers94,4824
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-58 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.486, 127.486, 327.064
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHELEULEU(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA3 - 1111 - 19
12THRTHRSERSER(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA13 - 2021 - 28
13THRTHRASNASN(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA23 - 3731 - 45
14THRTHRVALVAL(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA39 - 4347 - 51
15GLYGLYGLUGLU(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA45 - 4953 - 57
16LYSLYSTHRTHR(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA51 - 8859 - 96
17GLNGLNTHRTHR(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA90 - 9198 - 99
18ILEILEPROPRO(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA94 - 96102 - 104
19LEULEUILEILE(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA98 - 102106 - 110
110GLUGLULYSLYS(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA104 - 113112 - 121
111PHEPHELEULEU(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA116 - 152124 - 160
112VALVALLEULEU(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA154 - 179162 - 187
113TRPTRPTRPTRP(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA182 - 188190 - 196
114PHEPHEASPASP(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA190 - 192198 - 200
115GLNGLNLEULEU(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA194 - 195202 - 203
21PHEPHELEULEU(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB3 - 1111 - 19
22THRTHRSERSER(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB13 - 2021 - 28
23THRTHRASNASN(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB23 - 3731 - 45
24THRTHRVALVAL(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB39 - 4347 - 51
25GLYGLYGLUGLU(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB45 - 4953 - 57
26LYSLYSTHRTHR(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB51 - 8859 - 96
27GLNGLNTHRTHR(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB90 - 9198 - 99
28ILEILEPROPRO(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB94 - 96102 - 104
29LEULEUILEILE(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB98 - 102106 - 110
210GLUGLULYSLYS(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB104 - 113112 - 121
211PHEPHELEULEU(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB116 - 152124 - 160
212VALVALLEULEU(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB154 - 179162 - 187
213TRPTRPTRPTRP(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB182 - 188190 - 196
214PHEPHEASPASP(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB190 - 192198 - 200
215GLNGLNLEULEU(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB194 - 195202 - 203
31PHEPHELEULEU(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC3 - 1111 - 19
32THRTHRSERSER(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC13 - 2021 - 28
33THRTHRASNASN(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC23 - 3731 - 45
34THRTHRVALVAL(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC39 - 4347 - 51
35GLYGLYGLUGLU(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC45 - 4953 - 57
36LYSLYSTHRTHR(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC51 - 8859 - 96
37GLNGLNTHRTHR(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC90 - 9198 - 99
38ILEILEPROPRO(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC94 - 96102 - 104
39LEULEUILEILE(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC98 - 102106 - 110
310GLUGLULYSLYS(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC104 - 113112 - 121
311PHEPHELEULEU(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC116 - 152124 - 160
312VALVALLEULEU(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC154 - 179162 - 187
313TRPTRPTRPTRP(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC182 - 188190 - 196
314PHEPHEASPASP(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC190 - 192198 - 200
315GLNGLNLEULEU(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC194 - 195202 - 203
41PHEPHELEULEU(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD3 - 1111 - 19
42THRTHRSERSER(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD13 - 2021 - 28
43THRTHRASNASN(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD23 - 3731 - 45
44THRTHRVALVAL(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD39 - 4347 - 51
45GLYGLYGLUGLU(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD45 - 4953 - 57
46LYSLYSTHRTHR(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD51 - 8859 - 96
47GLNGLNTHRTHR(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD90 - 9198 - 99
48ILEILEPROPRO(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD94 - 96102 - 104
49LEULEUILEILE(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD98 - 102106 - 110
410GLUGLULYSLYS(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD104 - 113112 - 121
411PHEPHELEULEU(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD116 - 152124 - 160
412VALVALLEULEU(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD154 - 179162 - 187
413TRPTRPTRPTRP(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD182 - 188190 - 196
414PHEPHEASPASP(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD190 - 192198 - 200
415GLNGLNLEULEU(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD194 - 195202 - 203
51PHEPHELEULEU(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE3 - 1111 - 19
52THRTHRSERSER(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE13 - 2021 - 28
53THRTHRASNASN(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE23 - 3731 - 45
54THRTHRVALVAL(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE39 - 4347 - 51
55GLYGLYGLUGLU(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE45 - 4953 - 57
56LYSLYSTHRTHR(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE51 - 8859 - 96
57GLNGLNTHRTHR(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE90 - 9198 - 99
58ILEILEPROPRO(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE94 - 96102 - 104
59LEULEUILEILE(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE98 - 102106 - 110
510GLUGLULYSLYS(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE104 - 113112 - 121
511PHEPHELEULEU(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE116 - 152124 - 160
512VALVALLEULEU(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE154 - 179162 - 187
513TRPTRPTRPTRP(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE182 - 188190 - 196
514PHEPHEASPASP(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE190 - 192198 - 200
515GLNGLNLEULEU(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE194 - 195202 - 203
61PHEPHELEULEU(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF3 - 1111 - 19
62THRTHRSERSER(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF13 - 2021 - 28
63THRTHRASNASN(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF23 - 3731 - 45
64THRTHRVALVAL(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF39 - 4347 - 51
65GLYGLYGLUGLU(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF45 - 4953 - 57
66LYSLYSTHRTHR(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF51 - 8859 - 96
67GLNGLNTHRTHR(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF90 - 9198 - 99
68ILEILEPROPRO(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF94 - 96102 - 104
69LEULEUILEILE(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF98 - 102106 - 110
610GLUGLULYSLYS(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF104 - 113112 - 121
611PHEPHELEULEU(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF116 - 152124 - 160
612VALVALLEULEU(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF154 - 179162 - 187
613TRPTRPTRPTRP(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF182 - 188190 - 196
614PHEPHEASPASP(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF190 - 192198 - 200
615GLNGLNLEULEU(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF194 - 195202 - 203
71PHEPHELEULEU(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG3 - 1111 - 19
72THRTHRSERSER(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG13 - 2021 - 28
73THRTHRASNASN(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG23 - 3731 - 45
74THRTHRVALVAL(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG39 - 4347 - 51
75GLYGLYGLUGLU(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG45 - 4953 - 57
76LYSLYSTHRTHR(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG51 - 8859 - 96
77GLNGLNTHRTHR(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG90 - 9198 - 99
78ILEILEPROPRO(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG94 - 96102 - 104
79LEULEUILEILE(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG98 - 102106 - 110
710GLUGLULYSLYS(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG104 - 113112 - 121
711PHEPHELEULEU(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG116 - 152124 - 160
712VALVALLEULEU(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG154 - 179162 - 187
713TRPTRPTRPTRP(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG182 - 188190 - 196
714PHEPHEASPASP(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG190 - 192198 - 200
715GLNGLNLEULEU(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG194 - 195202 - 203
81PHEPHELEULEU(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH3 - 1111 - 19
82THRTHRSERSER(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH13 - 2021 - 28
83THRTHRASNASN(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH23 - 3731 - 45
84THRTHRVALVAL(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH39 - 4347 - 51
85GLYGLYGLUGLU(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH45 - 4953 - 57
86LYSLYSTHRTHR(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH51 - 8859 - 96
87GLNGLNTHRTHR(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH90 - 9198 - 99
88ILEILEPROPRO(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH94 - 96102 - 104
89LEULEUILEILE(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH98 - 102106 - 110
810GLUGLULYSLYS(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH104 - 113112 - 121
811PHEPHELEULEU(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH116 - 152124 - 160
812VALVALLEULEU(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH154 - 179162 - 187
813TRPTRPTRPTRP(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH182 - 188190 - 196
814PHEPHEASPASP(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH190 - 192198 - 200
815GLNGLNLEULEU(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH194 - 195202 - 203
91PHEPHELEULEU(chain I and (resseq 3:11 or resseq 13:21 or resseq...II3 - 1111 - 19
92THRTHRSERSER(chain I and (resseq 3:11 or resseq 13:21 or resseq...II13 - 2021 - 28
93THRTHRASNASN(chain I and (resseq 3:11 or resseq 13:21 or resseq...II23 - 3731 - 45
94THRTHRVALVAL(chain I and (resseq 3:11 or resseq 13:21 or resseq...II39 - 4347 - 51
95GLYGLYGLUGLU(chain I and (resseq 3:11 or resseq 13:21 or resseq...II45 - 4953 - 57
96LYSLYSTHRTHR(chain I and (resseq 3:11 or resseq 13:21 or resseq...II51 - 8859 - 96
97GLNGLNTHRTHR(chain I and (resseq 3:11 or resseq 13:21 or resseq...II90 - 9198 - 99
98ILEILEPROPRO(chain I and (resseq 3:11 or resseq 13:21 or resseq...II94 - 96102 - 104
99LEULEUILEILE(chain I and (resseq 3:11 or resseq 13:21 or resseq...II98 - 102106 - 110
910GLUGLULYSLYS(chain I and (resseq 3:11 or resseq 13:21 or resseq...II104 - 113112 - 121
911PHEPHELEULEU(chain I and (resseq 3:11 or resseq 13:21 or resseq...II116 - 152124 - 160
912VALVALLEULEU(chain I and (resseq 3:11 or resseq 13:21 or resseq...II154 - 179162 - 187
913TRPTRPTRPTRP(chain I and (resseq 3:11 or resseq 13:21 or resseq...II182 - 188190 - 196
914PHEPHEASPASP(chain I and (resseq 3:11 or resseq 13:21 or resseq...II190 - 192198 - 200
915GLNGLNLEULEU(chain I and (resseq 3:11 or resseq 13:21 or resseq...II194 - 195202 - 203
101PHEPHELEULEU(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ3 - 1111 - 19
102THRTHRSERSER(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ13 - 2021 - 28
103THRTHRASNASN(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ23 - 3731 - 45
104THRTHRVALVAL(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ39 - 4347 - 51
105GLYGLYGLUGLU(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ45 - 4953 - 57
106LYSLYSTHRTHR(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ51 - 8859 - 96
107GLNGLNTHRTHR(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ90 - 9198 - 99
108ILEILEPROPRO(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ94 - 96102 - 104
109LEULEUILEILE(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ98 - 102106 - 110
1010GLUGLULYSLYS(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ104 - 113112 - 121
1011PHEPHELEULEU(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ116 - 152124 - 160
1012VALVALLEULEU(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ154 - 179162 - 187
1013TRPTRPTRPTRP(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ182 - 188190 - 196
1014PHEPHEASPASP(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ190 - 192198 - 200
1015GLNGLNLEULEU(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ194 - 195202 - 203
111PHEPHELEULEU(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK3 - 1111 - 19
112THRTHRSERSER(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK13 - 2021 - 28
113THRTHRASNASN(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK23 - 3731 - 45
114THRTHRVALVAL(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK39 - 4347 - 51
115GLYGLYGLUGLU(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK45 - 4953 - 57
116LYSLYSTHRTHR(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK51 - 8859 - 96
117GLNGLNTHRTHR(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK90 - 9198 - 99
118ILEILEPROPRO(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK94 - 96102 - 104
119LEULEUILEILE(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK98 - 102106 - 110
1110GLUGLULYSLYS(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK104 - 113112 - 121
1111PHEPHELEULEU(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK116 - 152124 - 160
1112VALVALLEULEU(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK154 - 179162 - 187
1113TRPTRPTRPTRP(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK182 - 188190 - 196
1114PHEPHEASPASP(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK190 - 192198 - 200
1115GLNGLNLEULEU(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK194 - 195202 - 203
121PHEPHELEULEU(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL3 - 1111 - 19
122THRTHRSERSER(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL13 - 2021 - 28
123THRTHRASNASN(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL23 - 3731 - 45
124THRTHRVALVAL(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL39 - 4347 - 51
125GLYGLYGLUGLU(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL45 - 4953 - 57
126LYSLYSTHRTHR(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL51 - 8859 - 96
127GLNGLNTHRTHR(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL90 - 9198 - 99
128ILEILEPROPRO(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL94 - 96102 - 104
129LEULEUILEILE(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL98 - 102106 - 110
1210GLUGLULYSLYS(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL104 - 113112 - 121
1211PHEPHELEULEU(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL116 - 152124 - 160
1212VALVALLEULEU(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL154 - 179162 - 187
1213TRPTRPTRPTRP(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL182 - 188190 - 196
1214PHEPHEASPASP(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL190 - 192198 - 200
1215GLNGLNLEULEU(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL194 - 195202 - 203

-
Components

#1: Protein
Superoxide dismutase


Mass: 23620.486 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q5IZD9, superoxide dismutase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% (w/v) polyethylene glycol 4000, 5% (w/v) 2-propanol and 100 mM HEPES pH 7.5 and 1 mM hexammine cobalt (III) chloride as an additive

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 128266 / % possible obs: 100 % / Redundancy: 29.6 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.019 / Rrim(I) all: 0.115 / Χ2: 1.028 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.33-2.3721.20.67763620.9240.150.6931.373
2.37-2.4121.60.64364640.9410.1410.6581.414
2.41-2.4621.60.54663810.9520.120.5591.46
2.46-2.5121.60.51663910.9590.1140.5291.469
2.51-2.5621.60.48564090.9670.1060.4961.467
2.56-2.6221.60.44563780.9720.0980.4551.403
2.62-2.6921.60.37164080.9780.0810.381.362
2.69-2.7621.60.31564010.9830.0690.3231.258
2.76-2.8421.60.28564170.9860.0630.2921.229
2.84-2.9421.70.22363730.9910.0490.2281.164
2.94-3.0421.60.21364520.9910.0470.2181.449
3.04-3.1621.70.18163860.9940.040.1861.297
3.16-3.3123.80.15164030.9950.0310.1541.218
3.31-3.4843.10.14564070.9980.0220.1471.194
3.48-3.744.70.12764250.9980.0190.1291.024
3.7-3.9844.60.10464280.9990.0160.1050.677
3.98-4.3844.50.0964180.9990.0140.0910.762
4.38-5.0244.30.07964160.9990.0120.080.634
5.02-6.3244.10.07764470.9990.0120.0780.597
6.32-5043.40.06565000.9990.010.0650.311

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Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ISA

1isa


Resolution: 2.33000486301→36.5712467012 Å / SU ML: 0.299197773496 / Cross valid method: FREE R-VALUE / σ(F): 1.35409012865 / Phase error: 23.9266752481
RfactorNum. reflection% reflectionSelection details
Rfree0.247818808138 6498 5.08896685671 %Random selection
Rwork0.199588225603 ---
obs0.202041589108 127688 99.9945181879 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.0556487553 Å2
Refinement stepCycle: LAST / Resolution: 2.33000486301→36.5712467012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19394 0 12 882 20288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0080250932991319942
X-RAY DIFFRACTIONf_angle_d0.96647499158427163
X-RAY DIFFRACTIONf_chiral_restr0.05743749619872983
X-RAY DIFFRACTIONf_plane_restr0.006887727709123444
X-RAY DIFFRACTIONf_dihedral_angle_d16.008385222411597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.35650.3090920549922210.2416868546864076X-RAY DIFFRACTION100
2.3565-2.38420.2783739577922480.2247451092993962X-RAY DIFFRACTION100
2.3842-2.41330.2732218148752080.2275767854514056X-RAY DIFFRACTION100
2.4133-2.44380.2914243139832130.2193363323254027X-RAY DIFFRACTION100
2.4438-2.4760.2907352919442040.2167062232884026X-RAY DIFFRACTION99.9763649255
2.476-2.50990.2734930164632220.2219803506444062X-RAY DIFFRACTION100
2.5099-2.54570.2702510533591990.2201888289314049X-RAY DIFFRACTION100
2.5457-2.58370.2924506852522110.2192665168784005X-RAY DIFFRACTION100
2.5837-2.62410.2740071128321990.2168830500294057X-RAY DIFFRACTION100
2.6241-2.66710.2704983801452330.2192752119444038X-RAY DIFFRACTION100
2.6671-2.7130.310993462152020.2162660292684060X-RAY DIFFRACTION100
2.713-2.76240.2471194001842310.2153555064134022X-RAY DIFFRACTION100
2.7624-2.81550.2781754248492090.2190470533694026X-RAY DIFFRACTION100
2.8155-2.87290.288344863822230.2171944952744020X-RAY DIFFRACTION100
2.8729-2.93540.2387574078492260.2067211740074014X-RAY DIFFRACTION99.9764206555
2.9354-3.00360.278620058251960.2116903493854063X-RAY DIFFRACTION100
3.0036-3.07870.2670252747572180.2111256069444030X-RAY DIFFRACTION100
3.0787-3.16190.2266184612192500.2064054852084009X-RAY DIFFRACTION100
3.1619-3.25490.2634955679842020.2012982763824066X-RAY DIFFRACTION100
3.2549-3.35990.2580403817572120.1987252751494050X-RAY DIFFRACTION100
3.3599-3.47990.2521185087962340.2020334335314020X-RAY DIFFRACTION100
3.4799-3.61910.2638635519542290.2027144084224041X-RAY DIFFRACTION100
3.6191-3.78360.2184882312172070.1963292723614022X-RAY DIFFRACTION100
3.7836-3.98290.2516965572442170.1883304486954073X-RAY DIFFRACTION100
3.9829-4.23210.2269972359932150.1848557218364026X-RAY DIFFRACTION100
4.2321-4.55830.2147939994032390.1786675543964036X-RAY DIFFRACTION100
4.5583-5.0160.2191887495952300.180538651174005X-RAY DIFFRACTION100
5.016-5.73940.232348814761940.1875710971544080X-RAY DIFFRACTION100
5.7394-7.22190.2305326168971730.2021078391424099X-RAY DIFFRACTION100
7.2219-36.57570.2319438859762330.1850517239054070X-RAY DIFFRACTION99.8839368617

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