[English] 日本語
Yorodumi
- PDB-7npa: Crystal structure of the Coenzyme F420-dependent sulfite reductas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7npa
TitleCrystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution
ComponentsCoenzyme F420-dependent sulfite reductase
KeywordsOXIDOREDUCTASE / Sulfite detoxification / Sulfur metabolism / sulfide / hydrogenotrophic methanogens / iron-sulfur cluster / sulfite-reductase evolution / sulfite/nitrite reductase / siroheme / flavin / ferredoxin / F420 / thermophile
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily ...Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / 4Fe-4S binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / : / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / SIROHEME / Coenzyme F420-dependent sulfite reductase
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsJespersen, M. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society/ Germany
German Research Foundation (DFG)Schwerpunktprogram 1927 Iron-sulfur for Life WA 4053/1-1 Germany
Citation
Journal: Nat.Chem.Biol. / Year: 2023
Title: Structures of the sulfite detoxifying F 420 -dependent enzyme from Methanococcales.
Authors: Jespersen, M. / Pierik, A.J. / Wagner, T.
#1: Journal: Biorxiv / Year: 2022
Title: The structure of the F420-dependent sulfite-detoxifying enzyme from Methanococcales reveals a prototypical sulfite-reductase with assimilatory traits
Authors: Jespersen, M. / Pierik, A.J. / Wagner, T.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_refine_tls / pdbx_refine_tls_group
Item: _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y ..._pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.selection_details
Revision 2.0Dec 6, 2023Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coenzyme F420-dependent sulfite reductase
B: Coenzyme F420-dependent sulfite reductase
C: Coenzyme F420-dependent sulfite reductase
D: Coenzyme F420-dependent sulfite reductase
E: Coenzyme F420-dependent sulfite reductase
F: Coenzyme F420-dependent sulfite reductase
G: Coenzyme F420-dependent sulfite reductase
H: Coenzyme F420-dependent sulfite reductase
I: Coenzyme F420-dependent sulfite reductase
J: Coenzyme F420-dependent sulfite reductase
K: Coenzyme F420-dependent sulfite reductase
L: Coenzyme F420-dependent sulfite reductase
M: Coenzyme F420-dependent sulfite reductase
N: Coenzyme F420-dependent sulfite reductase
O: Coenzyme F420-dependent sulfite reductase
P: Coenzyme F420-dependent sulfite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,184,791375
Polymers1,107,92316
Non-polymers76,868359
Water194,05810772
1
A: Coenzyme F420-dependent sulfite reductase
B: Coenzyme F420-dependent sulfite reductase
C: Coenzyme F420-dependent sulfite reductase
D: Coenzyme F420-dependent sulfite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,378102
Polymers276,9814
Non-polymers19,39798
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47340 Å2
ΔGint-691 kcal/mol
Surface area90310 Å2
MethodPISA
2
E: Coenzyme F420-dependent sulfite reductase
F: Coenzyme F420-dependent sulfite reductase
G: Coenzyme F420-dependent sulfite reductase
H: Coenzyme F420-dependent sulfite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,58789
Polymers276,9814
Non-polymers18,60785
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45540 Å2
ΔGint-740 kcal/mol
Surface area90570 Å2
MethodPISA
3
I: Coenzyme F420-dependent sulfite reductase
J: Coenzyme F420-dependent sulfite reductase
K: Coenzyme F420-dependent sulfite reductase
L: Coenzyme F420-dependent sulfite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,69189
Polymers276,9814
Non-polymers18,71185
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45260 Å2
ΔGint-743 kcal/mol
Surface area90380 Å2
MethodPISA
4
M: Coenzyme F420-dependent sulfite reductase
N: Coenzyme F420-dependent sulfite reductase
O: Coenzyme F420-dependent sulfite reductase
P: Coenzyme F420-dependent sulfite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,13595
Polymers276,9814
Non-polymers20,15491
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46550 Å2
ΔGint-764 kcal/mol
Surface area90720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.148, 124.157, 241.062
Angle α, β, γ (deg.)102.280, 95.710, 90.250
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 4 or resid 6...
21(chain B and (resid 2 through 4 or resid 6...
31(chain C and (resid 2 through 4 or resid 6...
41(chain D and (resid 2 through 4 or resid 6...
51(chain E and (resid 2 through 4 or resid 6...
61(chain F and (resid 2 through 4 or resid 6...
71(chain G and (resid 2 through 4 or resid 6...
81(chain H and (resid 2 through 4 or resid 6...
91(chain I and (resid 2 through 4 or resid 6...
101(chain J and (resid 2 through 4 or resid 6...
111(chain K and (resid 2 through 4 or resid 6...
121(chain L and (resid 2 through 4 or resid 6...
131(chain M and (resid 2 through 4 or resid 6...
141(chain N and (resid 2 through 4 or resid 6...
151(chain O and (resid 2 through 4 or resid 6...
161(chain P and (resid 2 through 4 or resid 6...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 4 or resid 6...A2 - 4
121(chain A and (resid 2 through 4 or resid 6...A6 - 60
131(chain A and (resid 2 through 4 or resid 6...A62 - 70
141(chain A and (resid 2 through 4 or resid 6...A452
151(chain A and (resid 2 through 4 or resid 6...A1 - 618
161(chain A and (resid 2 through 4 or resid 6...A6 - 510
171(chain A and (resid 2 through 4 or resid 6...A512 - 514
181(chain A and (resid 2 through 4 or resid 6...A530 - 568
191(chain A and (resid 2 through 4 or resid 6...A613 - 611
1101(chain A and (resid 2 through 4 or resid 6...A613 - 618
1111(chain A and (resid 2 through 4 or resid 6...A1201 - 1601
211(chain B and (resid 2 through 4 or resid 6...B2 - 4
221(chain B and (resid 2 through 4 or resid 6...B6 - 60
231(chain B and (resid 2 through 4 or resid 6...B62 - 70
241(chain B and (resid 2 through 4 or resid 6...B1 - 618
251(chain B and (resid 2 through 4 or resid 6...B0
261(chain B and (resid 2 through 4 or resid 6...B454
271(chain B and (resid 2 through 4 or resid 6...B0
281(chain B and (resid 2 through 4 or resid 6...B1 - 618
291(chain B and (resid 2 through 4 or resid 6...B530 - 568
2101(chain B and (resid 2 through 4 or resid 6...B585 - 611
2111(chain B and (resid 2 through 4 or resid 6...B613 - 618
2121(chain B and (resid 2 through 4 or resid 6...B1201 - 1601
311(chain C and (resid 2 through 4 or resid 6...C2 - 4
321(chain C and (resid 2 through 4 or resid 6...C6 - 60
331(chain C and (resid 2 through 4 or resid 6...C62 - 70
341(chain C and (resid 2 through 4 or resid 6...C454
351(chain C and (resid 2 through 4 or resid 6...C452
361(chain C and (resid 2 through 4 or resid 6...C1 - 618
371(chain C and (resid 2 through 4 or resid 6...C1 - 618
381(chain C and (resid 2 through 4 or resid 6...C516 - 528
391(chain C and (resid 2 through 4 or resid 6...C530 - 568
3101(chain C and (resid 2 through 4 or resid 6...C613 - 611
3111(chain C and (resid 2 through 4 or resid 6...C613 - 618
3121(chain C and (resid 2 through 4 or resid 6...C1201 - 1601
411(chain D and (resid 2 through 4 or resid 6...D2 - 4
421(chain D and (resid 2 through 4 or resid 6...D6 - 60
431(chain D and (resid 2 through 4 or resid 6...D62 - 70
441(chain D and (resid 2 through 4 or resid 6...D452
451(chain D and (resid 2 through 4 or resid 6...D2 - 618
461(chain D and (resid 2 through 4 or resid 6...D6 - 510
471(chain D and (resid 2 through 4 or resid 6...D512 - 514
481(chain D and (resid 2 through 4 or resid 6...D530 - 568
491(chain D and (resid 2 through 4 or resid 6...D613 - 611
4101(chain D and (resid 2 through 4 or resid 6...D613 - 617
4111(chain D and (resid 2 through 4 or resid 6...D618
4121(chain D and (resid 2 through 4 or resid 6...D2 - 618
4131(chain D and (resid 2 through 4 or resid 6...D2 - 618
4141(chain D and (resid 2 through 4 or resid 6...D2 - 618
4151(chain D and (resid 2 through 4 or resid 6...D2 - 618
4161(chain D and (resid 2 through 4 or resid 6...D2 - 618
4171(chain D and (resid 2 through 4 or resid 6...D2 - 618
4181(chain D and (resid 2 through 4 or resid 6...D2 - 618
4191(chain D and (resid 2 through 4 or resid 6...D2 - 618
511(chain E and (resid 2 through 4 or resid 6...E2 - 4
521(chain E and (resid 2 through 4 or resid 6...E6 - 60
531(chain E and (resid 2 through 4 or resid 6...E62 - 70
541(chain E and (resid 2 through 4 or resid 6...E311
551(chain E and (resid 2 through 4 or resid 6...E337 - 452
561(chain E and (resid 2 through 4 or resid 6...E454
571(chain E and (resid 2 through 4 or resid 6...E456 - 510
581(chain E and (resid 2 through 4 or resid 6...E512 - 514
591(chain E and (resid 2 through 4 or resid 6...E516 - 528
5101(chain E and (resid 2 through 4 or resid 6...E530 - 568
5111(chain E and (resid 2 through 4 or resid 6...E570 - 583
5121(chain E and (resid 2 through 4 or resid 6...E585 - 611
5131(chain E and (resid 2 through 4 or resid 6...E613 - 618
5141(chain E and (resid 2 through 4 or resid 6...E1201 - 1601
611(chain F and (resid 2 through 4 or resid 6...F2 - 4
621(chain F and (resid 2 through 4 or resid 6...F6 - 60
631(chain F and (resid 2 through 4 or resid 6...F62 - 70
641(chain F and (resid 2 through 4 or resid 6...F311
651(chain F and (resid 2 through 4 or resid 6...F1 - 618
661(chain F and (resid 2 through 4 or resid 6...F1 - 618
671(chain F and (resid 2 through 4 or resid 6...F1 - 618
681(chain F and (resid 2 through 4 or resid 6...F1 - 618
691(chain F and (resid 2 through 4 or resid 6...F516 - 528
6101(chain F and (resid 2 through 4 or resid 6...F0
6111(chain F and (resid 2 through 4 or resid 6...F1 - 618
6121(chain F and (resid 2 through 4 or resid 6...F613 - 618
6131(chain F and (resid 2 through 4 or resid 6...F1201 - 8
6141(chain F and (resid 2 through 4 or resid 6...F1201 - 1601
711(chain G and (resid 2 through 4 or resid 6...G2 - 4
721(chain G and (resid 2 through 4 or resid 6...G6 - 60
731(chain G and (resid 2 through 4 or resid 6...G0
741(chain G and (resid 2 through 4 or resid 6...G452
751(chain G and (resid 2 through 4 or resid 6...G1 - 618
761(chain G and (resid 2 through 4 or resid 6...G6 - 510
771(chain G and (resid 2 through 4 or resid 6...G512 - 514
781(chain G and (resid 2 through 4 or resid 6...G530 - 568
791(chain G and (resid 2 through 4 or resid 6...G613 - 611
7101(chain G and (resid 2 through 4 or resid 6...G613 - 618
7111(chain G and (resid 2 through 4 or resid 6...G1201 - 1601
811(chain H and (resid 2 through 4 or resid 6...H2 - 4
821(chain H and (resid 2 through 4 or resid 6...H6 - 60
831(chain H and (resid 2 through 4 or resid 6...H62 - 70
841(chain H and (resid 2 through 4 or resid 6...H2 - 618
851(chain H and (resid 2 through 4 or resid 6...H0
861(chain H and (resid 2 through 4 or resid 6...H454
871(chain H and (resid 2 through 4 or resid 6...H0
881(chain H and (resid 2 through 4 or resid 6...H2 - 618
891(chain H and (resid 2 through 4 or resid 6...H530 - 568
8101(chain H and (resid 2 through 4 or resid 6...H585 - 611
8111(chain H and (resid 2 through 4 or resid 6...H613 - 618
8121(chain H and (resid 2 through 4 or resid 6...H1201 - 1601
911(chain I and (resid 2 through 4 or resid 6...I2 - 4
921(chain I and (resid 2 through 4 or resid 6...I6 - 60
931(chain I and (resid 2 through 4 or resid 6...I62 - 70
941(chain I and (resid 2 through 4 or resid 6...I311
951(chain I and (resid 2 through 4 or resid 6...I337 - 452
961(chain I and (resid 2 through 4 or resid 6...I454
971(chain I and (resid 2 through 4 or resid 6...I456 - 510
981(chain I and (resid 2 through 4 or resid 6...I512 - 514
991(chain I and (resid 2 through 4 or resid 6...I516 - 528
9101(chain I and (resid 2 through 4 or resid 6...I530 - 568
9111(chain I and (resid 2 through 4 or resid 6...I570 - 583
9121(chain I and (resid 2 through 4 or resid 6...I585 - 611
9131(chain I and (resid 2 through 4 or resid 6...I613 - 618
9141(chain I and (resid 2 through 4 or resid 6...I1201 - 1601
1011(chain J and (resid 2 through 4 or resid 6...J2 - 4
1021(chain J and (resid 2 through 4 or resid 6...J6 - 60
1031(chain J and (resid 2 through 4 or resid 6...J0
1041(chain J and (resid 2 through 4 or resid 6...J1 - 618
1051(chain J and (resid 2 through 4 or resid 6...J456 - 510
1061(chain J and (resid 2 through 4 or resid 6...J6 - 510
1071(chain J and (resid 2 through 4 or resid 6...J512 - 514
1081(chain J and (resid 2 through 4 or resid 6...J516 - 528
1091(chain J and (resid 2 through 4 or resid 6...J570 - 583
10101(chain J and (resid 2 through 4 or resid 6...J613 - 6
10111(chain J and (resid 2 through 4 or resid 6...J613 - 617
10121(chain J and (resid 2 through 4 or resid 6...J618
10131(chain J and (resid 2 through 4 or resid 6...J1 - 618
10141(chain J and (resid 2 through 4 or resid 6...J1 - 618
10151(chain J and (resid 2 through 4 or resid 6...J1 - 618
10161(chain J and (resid 2 through 4 or resid 6...J1 - 618
10171(chain J and (resid 2 through 4 or resid 6...J1 - 618
10181(chain J and (resid 2 through 4 or resid 6...J1 - 618
10191(chain J and (resid 2 through 4 or resid 6...J1 - 618
1111(chain K and (resid 2 through 4 or resid 6...K2 - 4
1121(chain K and (resid 2 through 4 or resid 6...K6 - 60
1131(chain K and (resid 2 through 4 or resid 6...K62 - 70
1141(chain K and (resid 2 through 4 or resid 6...K2 - 618
1151(chain K and (resid 2 through 4 or resid 6...K0
1161(chain K and (resid 2 through 4 or resid 6...K454
1171(chain K and (resid 2 through 4 or resid 6...K0
1181(chain K and (resid 2 through 4 or resid 6...K2 - 618
1191(chain K and (resid 2 through 4 or resid 6...K530 - 568
11101(chain K and (resid 2 through 4 or resid 6...K585 - 611
11111(chain K and (resid 2 through 4 or resid 6...K613 - 618
11121(chain K and (resid 2 through 4 or resid 6...K1201 - 1601
1211(chain L and (resid 2 through 4 or resid 6...L2 - 4
1221(chain L and (resid 2 through 4 or resid 6...L6 - 60
1231(chain L and (resid 2 through 4 or resid 6...L62 - 70
1241(chain L and (resid 2 through 4 or resid 6...L2 - 618
1251(chain L and (resid 2 through 4 or resid 6...L0
1261(chain L and (resid 2 through 4 or resid 6...L454
1271(chain L and (resid 2 through 4 or resid 6...L0
1281(chain L and (resid 2 through 4 or resid 6...L2 - 618
1291(chain L and (resid 2 through 4 or resid 6...L530 - 568
12101(chain L and (resid 2 through 4 or resid 6...L585 - 611
12111(chain L and (resid 2 through 4 or resid 6...L613 - 618
12121(chain L and (resid 2 through 4 or resid 6...L1201 - 1601
1311(chain M and (resid 2 through 4 or resid 6...M2 - 4
1321(chain M and (resid 2 through 4 or resid 6...M6 - 60
1331(chain M and (resid 2 through 4 or resid 6...M62 - 70
1341(chain M and (resid 2 through 4 or resid 6...M311
1351(chain M and (resid 2 through 4 or resid 6...M337 - 452
1361(chain M and (resid 2 through 4 or resid 6...M454
1371(chain M and (resid 2 through 4 or resid 6...M456 - 510
1381(chain M and (resid 2 through 4 or resid 6...M512 - 514
1391(chain M and (resid 2 through 4 or resid 6...M516 - 528
13101(chain M and (resid 2 through 4 or resid 6...M530 - 568
13111(chain M and (resid 2 through 4 or resid 6...M570 - 583
13121(chain M and (resid 2 through 4 or resid 6...M585 - 611
13131(chain M and (resid 2 through 4 or resid 6...M613 - 618
13141(chain M and (resid 2 through 4 or resid 6...M1201 - 1601
1411(chain N and (resid 2 through 4 or resid 6...N2 - 4
1421(chain N and (resid 2 through 4 or resid 6...N6 - 60
1431(chain N and (resid 2 through 4 or resid 6...N62 - 70
1441(chain N and (resid 2 through 4 or resid 6...N311
1451(chain N and (resid 2 through 4 or resid 6...N2 - 618
1461(chain N and (resid 2 through 4 or resid 6...N2 - 618
1471(chain N and (resid 2 through 4 or resid 6...N2 - 618
1481(chain N and (resid 2 through 4 or resid 6...N2 - 618
1491(chain N and (resid 2 through 4 or resid 6...N516 - 528
14101(chain N and (resid 2 through 4 or resid 6...N0
14111(chain N and (resid 2 through 4 or resid 6...N2 - 618
14121(chain N and (resid 2 through 4 or resid 6...N613 - 618
14131(chain N and (resid 2 through 4 or resid 6...N1201 - 8
14141(chain N and (resid 2 through 4 or resid 6...N1201 - 1601
1511(chain O and (resid 2 through 4 or resid 6...O2 - 4
1521(chain O and (resid 2 through 4 or resid 6...O6 - 60
1531(chain O and (resid 2 through 4 or resid 6...O0
1541(chain O and (resid 2 through 4 or resid 6...O452
1551(chain O and (resid 2 through 4 or resid 6...O2 - 618
1561(chain O and (resid 2 through 4 or resid 6...O6 - 510
1571(chain O and (resid 2 through 4 or resid 6...O512 - 514
1581(chain O and (resid 2 through 4 or resid 6...O530 - 568
1591(chain O and (resid 2 through 4 or resid 6...O613 - 611
15101(chain O and (resid 2 through 4 or resid 6...O613 - 618
15111(chain O and (resid 2 through 4 or resid 6...O1201 - 1601
1611(chain P and (resid 2 through 4 or resid 6...P2 - 4
1621(chain P and (resid 2 through 4 or resid 6...P6 - 60
1631(chain P and (resid 2 through 4 or resid 6...P62 - 70
1641(chain P and (resid 2 through 4 or resid 6...P2 - 618
1651(chain P and (resid 2 through 4 or resid 6...P0
1661(chain P and (resid 2 through 4 or resid 6...P454
1671(chain P and (resid 2 through 4 or resid 6...P0
1681(chain P and (resid 2 through 4 or resid 6...P2 - 618
1691(chain P and (resid 2 through 4 or resid 6...P530 - 568
16101(chain P and (resid 2 through 4 or resid 6...P585 - 611
16111(chain P and (resid 2 through 4 or resid 6...P613 - 618
16121(chain P and (resid 2 through 4 or resid 6...P1201 - 1601

-
Components

-
Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein
Coenzyme F420-dependent sulfite reductase


Mass: 69245.164 Da / Num. of mol.: 16 / Mutation: wild-type / Source method: isolated from a natural source / Details: /
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: /
References: UniProt: A0A2Z5PF12, sulfite reductase (coenzyme F420)

-
Non-polymers , 12 types, 11131 molecules

#2: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 97 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 123 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SRM / SIROHEME / Siroheme


Mass: 916.661 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C42H44FeN4O16 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Li
#11: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#12: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10772 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.68 % / Description: Thick square-shaped brown crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Fsr from Methanothermococcus thermolithotrophicus was crystallized anaerobically under yellow light at a concentration of 11 mg ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM ...Details: Fsr from Methanothermococcus thermolithotrophicus was crystallized anaerobically under yellow light at a concentration of 11 mg ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol, 0.5 mM FAD and 0.0155 mM F420H2. 0.6 ul of sample was mixed with 0.6 ul reservoir solution. The reservoir solution contained 0.2 M Lithium sulfate, 0.1 M Bis-Tris, pH 5.5 and 25 % w/v Polyethylene glycol 3350. Crystals appeared after few days.
PH range: / / Temp details: +/- 1 degree of oscillation

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.55→121.276 Å / Num. obs: 1396397 / % possible obs: 94.5 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.075 / Rrim(I) all: 0.198 / Net I/σ(I): 8.7
Reflection shellResolution: 1.55→1.689 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.623 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 69018 / CC1/2: 0.439 / Rpim(I) all: 0.664 / Rrim(I) all: 1.755 / % possible all: 70.9

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NP8

7np8


Resolution: 1.55→77.29 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 18.34 / Stereochemistry target values: ML
Details: The last refinement cycles were performed with hydrogens in riding position.
RfactorNum. reflection% reflection
Rfree0.1711 69210 4.96 %
Rwork0.1588 1326976 -
obs0.1594 1396186 75.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.69 Å2 / Biso mean: 26.3738 Å2 / Biso min: 5.3 Å2
Refinement stepCycle: final / Resolution: 1.55→77.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms77290 0 3554 10774 91618
Biso mean--23.43 35.95 -
Num. residues----9879
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A26768X-RAY DIFFRACTION7.14TORSIONAL
12B26768X-RAY DIFFRACTION7.14TORSIONAL
13C26768X-RAY DIFFRACTION7.14TORSIONAL
14D26768X-RAY DIFFRACTION7.14TORSIONAL
15E26768X-RAY DIFFRACTION7.14TORSIONAL
16F26768X-RAY DIFFRACTION7.14TORSIONAL
17G26768X-RAY DIFFRACTION7.14TORSIONAL
18H26768X-RAY DIFFRACTION7.14TORSIONAL
19I26768X-RAY DIFFRACTION7.14TORSIONAL
110J26768X-RAY DIFFRACTION7.14TORSIONAL
111K26768X-RAY DIFFRACTION7.14TORSIONAL
112L26768X-RAY DIFFRACTION7.14TORSIONAL
113M26768X-RAY DIFFRACTION7.14TORSIONAL
114N26768X-RAY DIFFRACTION7.14TORSIONAL
115O26768X-RAY DIFFRACTION7.14TORSIONAL
116P26768X-RAY DIFFRACTION7.14TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.570.3369900.3033170417943
1.57-1.590.33221700.3014323234026
1.59-1.610.32623200.2835637595710
1.61-1.630.31354550.28838854930915
1.63-1.650.29866740.2847122801295421
1.65-1.670.29658600.2785169181777829
1.67-1.690.283811950.2703225712376639
1.69-1.720.28615600.2635286323019249
1.72-1.750.277119990.2549371993919864
1.75-1.780.271624020.2535457854818778
1.78-1.810.256426350.2459511645379987
1.81-1.840.244827490.2318536795642892
1.84-1.870.238127880.2198555885837695
1.87-1.910.228529640.214571866015098
1.91-1.950.210630210.1965573126033398
1.95-20.212228700.1847575956046598
2-2.050.190228780.1738576466052498
2.05-2.10.183730180.1642576236064198
2.1-2.170.166929990.153576266062598
2.17-2.240.171331110.1489575806069199
2.24-2.320.157830680.1399577306079899
2.32-2.410.15930850.1426579266101199
2.41-2.520.152730980.1392577916088999
2.52-2.650.153129570.1402580726102999
2.65-2.820.161630080.1451581946120299
2.82-3.040.155329830.1458582166119999
3.04-3.340.152430770.1424582066128399
3.34-3.820.137730850.13045824761332100
3.82-4.820.120130080.11355850861516100
4.82-77.290.151230830.15015827561358100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.99440.4419-0.17130.7812-0.110.6630.0581-0.171-0.07550.0922-0.08330.00080.0452-0.0280.01960.087-0.02030.00250.12110.00490.093366.98350.579-64.669
20.18150.044-0.23730.1319-0.06850.8624-0.00670.0293-0.0017-0.0115-0.00770.02370.0397-0.06350.02560.0694-0.001-0.01110.06910.00850.090678.64959.802-104.886
31.3779-0.5651-0.29550.7951-0.36270.96760.0370.2039-0.0648-0.1012-0.03380.08790.05-0.09620.00650.1113-0.0048-0.0310.12560.04660.106277.73976.669-141.999
42.7374-0.54360.20841.80880.12440.8981-0.00670.12940.34850.0530.0598-0.0371-0.3895-0.0275-0.01130.28770.0422-0.03140.11120.06260.225376.108106.543-141.474
52.37110.05110.68131.0235-0.40771.14650.03550.25850.1645-0.0737-0.1177-0.0736-0.22670.040.06390.20490.0336-0.01220.19870.09120.17881.14495.161-152.215
60.7605-0.46740.43411.1105-0.56371.10130.02550.12190.0649-0.048-0.00140.1237-0.138-0.1809-0.00970.16080.0396-0.02480.19610.04970.139370.24491.382-146.667
71.99120.70380.13573.44230.14721.04860.0481-0.02670.20270.1635-0.03340.3258-0.265-0.2577-0.00910.21080.08160.00380.19960.04290.111664.24395.173-135.94
80.353-0.01850.27020.1675-0.13821.0573-0.00150.02490.0323-0.01120.01480.0551-0.0971-0.1290.00390.08530.0193-0.00030.08020.0120.111674.71577.766-104.272
90.12380.06360.3770.0843-0.14533.9723-0.00070.01290.06080.03140.00050.016-0.1961-0.08620.01140.08760.00360.00070.07450.01290.117889.55878.685-90.171
101.3629-0.1545-0.47950.84360.32372.71850.0177-0.01310.1854-0.00670.0043-0.0373-0.28490.1308-0.03290.1177-0.0139-0.01280.07560.03740.122692.97688.085-111.177
111.11580.59790.0631.08240.24450.82640.086-0.15660.1170.1396-0.10110.0468-0.1077-0.00490.01440.141-0.0508-0.0090.1380.0040.1168123.57286.321-63.191
120.78680.29640.07490.71620.17440.55080.0463-0.13820.06240.0923-0.044-0.0944-0.06840.1048-0.00030.1785-0.0681-0.02270.16920.02580.1279134.17187.708-65.16
130.20360.05860.15070.21140.05470.75240.00380.03820.0326-0.0014-0.0143-0.034-0.07720.10610.01980.0832-0.01720.00390.08990.0250.1008119.55875.864-104.217
140.9227-0.2275-0.20221.1137-0.01150.8972-0.00390.2112-0.1952-0.3218-0.0627-0.14970.20730.10130.02980.24240.04960.06370.1989-0.02610.1768124.9543.107-143.521
150.2649-0.0058-0.2070.18660.03780.633-0.00660.0009-0.0495-0.0291-0.0188-0.05250.07060.10440.02650.08410.0181-0.00090.09990.02230.1165119.98253.084-106.996
161.4901-0.4450.31130.827-0.16690.91-0.0605-0.2056-0.08880.27740.099-0.19730.25670.2231-0.00770.27810.0808-0.06410.19220.01880.208863.437-20.237-59.261
170.1719-0.02750.04810.423-0.01030.82620.00980.0088-0.0538-0.0164-0.0111-0.08780.16620.14530.01390.10340.02910.02180.109-0.00510.158155.507-16.038-96.624
180.68750.43040.31611.14250.19340.88720.0080.1468-0.0378-0.4378-0.04180.2962-0.0328-0.1280.04250.38170.0308-0.09470.2185-0.090.258424.357-17.877-139.755
190.3665-0.09710.19890.54890.2690.84490.06850.1339-0.1665-0.1852-0.10430.18530.1863-0.1491-0.0110.324-0.0206-0.02730.2122-0.10320.302226.78-33.358-130.902
200.17030.02690.1220.29230.20590.8838-0.0031-0.0008-0.0661-0.006-0.03780.05510.097-0.11470.06050.0778-0.02520.01490.0844-0.01350.1430.759-9.078-96.597
211.3511-0.5694-0.24780.98420.06550.863-0.0899-0.1691-0.0430.12670.0370.12830.036-0.06430.04490.0939-0.00520.01380.0973-0.01720.101822.18828.268-63.248
220.7122-0.2146-0.28740.30180.37361.8592-0.0891-0.35660.31180.25460.0555-0.0225-0.2839-0.06390.01710.28560.0567-0.02930.2652-0.11020.276116.31446.369-54.831
230.1668-0.0659-0.14170.29690.21950.64310.00360.00590.0588-0.0523-0.03260.0492-0.1317-0.04230.01790.09130.0014-0.02160.07720.00280.112229.81636.685-90.437
240.2986-0.0263-0.25440.27810.16221.4816-0.01430.0558-0.0135-0.0755-0.030.05650.0454-0.14680.06950.0974-0.0146-0.01710.0737-0.00760.108729.55913.662-109.812
250.96640.5345-0.26950.8689-0.10110.8233-0.05670.1776-0.0462-0.25450.0819-0.1517-0.05580.0895-0.02350.2679-0.0270.0670.17650.00630.14562.08128.434-140.27
260.03370.0308-0.13680.0342-0.1520.753-0.04180.30430.2656-0.35170.12050.0448-0.32380.0727-0.08560.5438-0.11620.06160.35960.10770.281866.52147.09-148.802
271.7457-0.1266-0.05110.60990.04070.6850.0471-0.01380.2367-0.03760.0218-0.1076-0.25250.11760.00310.318-0.06390.08550.21580.02460.192366.19344.348-132.124
280.19-0.0386-0.0790.248-0.06710.717-0.00180.03650.0242-0.0495-0.0185-0.0654-0.09510.06640.02370.0851-0.02810.00970.08630.01030.112552.27825.71-100.802
291.03380.4922-0.07480.6648-0.14470.40570.0826-0.1945-0.06770.1076-0.1088-0.01310.0518-0.02570.02740.1673-0.08580.01550.2185-0.02680.126559.82321.5152.52
300.13070.0173-0.20820.2408-0.06020.74430.00210.0430.00850.0003-0.0570.03940.1022-0.19570.05580.0971-0.03570.00980.1851-0.03370.10569.33532.49512.489
310.9421-0.40090.28740.9575-0.22190.70550.01830.11250.2003-0.1916-0.1344-0.0279-0.2029-0.16070.09740.22660.1125-0.0280.26130.01520.164468.05362.976-24.848
320.1711-0.02690.26930.4784-0.06760.5341-0.0579-0.01780.1875-0.2299-0.12030.2831-0.2865-0.4230.08420.35050.2194-0.12450.5116-0.08260.354451.21469.882-25.476
330.1936-0.04470.03310.1641-0.00140.56960.00020.03930.0255-0.0316-0.05150.0277-0.038-0.22950.04820.07940.01820.00310.1973-0.02210.125171.36952.66614.318
341.04790.59630.05961.14380.33220.73770.0363-0.1030.040.0466-0.0767-0.0533-0.0255-0.03240.0460.05520.0093-0.02040.09710.01950.1323116.61654.22849.515
355.023-0.56431.86531.0281-0.03131.51030.0161-0.33790.17320.1084-0.09060.1633-0.1113-0.23830.05760.10740.00280.00730.1417-0.02750.1766115.2763.81960.02
361.14020.44810.35220.78390.3210.8729-0.0082-0.08640.0420.03590.0056-0.0829-0.03140.05860.00440.0870.0057-0.01050.08980.02370.15124.92258.14353.673
371.2557-0.0422-0.08053.2510.05450.77210.0290.03610.1121-0.1486-0.0577-0.3084-0.09040.09190.03290.1128-0.0355-0.02150.12360.02990.1231130.5860.40742.66
380.25890.05110.39140.1780.00480.9560.0210.0634-0.0088-0.0054-0.0093-0.09450.01110.1396-0.00170.07120.02160.01820.11390.02160.152119.08545.36417.277
390.06410.06950.38550.40110.51262.2174-0.01830.02820.0184-0.1128-0.0101-0.0356-0.15750.00150.0370.08840.02840.0240.12530.02480.13499.52751.334-1.393
403.4833-0.51840.80693.9043-1.50723.3956-0.00770.0220.16330.02250.0390.1411-0.2365-0.2025-0.06010.06350.02680.01390.0857-0.02520.102297.32257.88622.299
410.757-0.4666-0.11711.1410.34621.06970.06150.1427-0.069-0.1594-0.07390.0220.1096-0.01420.00860.16770.04380.04930.17950.00420.1356109.70419.208-28.794
420.4508-0.169-0.31510.75970.26431.25560.01920.05620.0024-0.1146-0.0105-0.12890.15290.2044-0.02070.1930.06550.05330.1830.01740.1546117.95716.767-30.256
431.81360.7865-0.17562.9178-0.14181.11770.0578-0.1044-0.08740.0545-0.0076-0.28360.21610.2881-0.03980.23060.10.03710.2326-0.00610.1309124.01613.223-19.53
440.20160.0048-0.08350.18150.12320.82630.01030.0229-0.0303-0.0137-0.0145-0.06830.12090.05810.01150.0950.02620.01040.07990.0140.1224108.12928.55512.614
451.1332-0.3423-0.10361.87280.23591.0098-0.087-0.1398-0.10830.2425-0.02290.00140.0529-0.01490.11250.1109-0.00160.0120.07990.04740.16242.458-44.82852.051
461.0683-0.18240.11111.48340.2321.2448-0.01450.0075-0.01680.0319-0.0794-0.26050.03470.31670.06790.12590.01510.01930.2870.18850.47471.988-48.78949.235
470.89770.32970.05824.1428-1.47731.0775-0.0598-0.1811-0.00880.3121-0.1085-0.3046-0.17470.23160.12170.1947-0.0326-0.07110.22160.10590.334361.752-43.74561.087
481.0521-0.76950.34440.802-0.36230.722-0.0584-0.02290.00850.1124-0.0828-0.1888-0.04020.09250.13220.1342-0.00520.00250.10830.06270.224452.507-41.21248.397
490.139-0.0415-0.12070.0289-0.06880.997-0.0698-0.1551-0.19690.0911-0.1502-0.20890.3360.17480.05860.28880.03990.02450.22840.15810.412359.908-63.20959.794
502.57470.4054-0.39770.35960.0560.472-0.09420.1193-0.3527-0.0677-0.0862-0.23790.19880.12650.14020.18340.05010.06570.19320.10380.383759.16-59.34943.861
510.1876-0.0761-0.0130.2835-0.10040.5794-0.06920.044-0.1618-0.0375-0.0621-0.00170.247-0.05760.11440.1617-0.02520.05360.1019-0.03640.206441.573-49.4819.414
520.4558-0.19510.40910.4933-0.01982.7127-0.00460.094-0.0343-0.1008-0.0691-0.0013-0.06130.07570.07380.0871-0.00990.00350.0763-0.01920.125146.172-28.6666.587
530.28120.20580.18140.23240.03060.16710.05020.1191-0.0233-0.205-0.03650.28130.0778-0.09450.090.33290.068-0.25410.3652-0.37960.31849.348-42.902-24.276
540.3523-0.17620.05690.2293-0.24210.31430.1115-0.03850.0047-0.1752-0.00130.120.2561-0.0315-0.12630.3536-0.0414-0.08360.3799-0.2230.46978.147-59.589-24.787
550.1919-0.0854-0.05410.25040.14280.652-0.0620.1086-0.1385-0.0283-0.11390.11450.1165-0.21670.10830.1242-0.05550.02510.1847-0.11070.249323.566-40.84515.109
561.4078-0.2329-0.16571.81110.05791.2321-0.0288-0.1552-0.01550.35570.00160.008-0.06510.08290.04240.1358-0.00960.01470.0654-0.01330.090626.3980.58853.926
571.2932-0.46280.18372.05490.12951.4397-0.0221-0.0846-0.18120.20610.02180.4244-0.0182-0.39890.07260.13820.03820.06850.2271-0.02720.3339-3.115.12253.452
581.00940.04190.24963.04190.89191.6957-0.0945-0.1969-0.15290.43770.06550.21850.1019-0.22490.02150.27460.01520.11690.16670.02730.23477.743-1.06464.075
591.2681-0.5056-0.32920.88650.3670.9965-0.0601-0.16250.11460.26190.04520.0854-0.1648-0.06990.01720.22850.02120.03080.1173-0.02180.161312.579.51358.632
604.20360.30770.26831.29170.04480.7818-0.01140.05690.30770.0042-0.01910.2653-0.193-0.12610.04130.19160.04310.03170.1276-0.01080.12429.38315.88748.008
610.31650.0945-0.06160.47750.19021.280.07780.0670.063-0.0873-0.08050.0863-0.2424-0.09680.01950.16220.0528-0.02280.1075-0.00940.143826.07411.53524.678
620.1346-0.0455-0.09010.23670.1161.11860.06780.1718-0.0709-0.185-0.12640.1704-0.0632-0.21780.04180.17560.0735-0.09380.2206-0.06740.160821.482-9.7494.923
631.45320.1120.37431.27710.12151.29260.01680.0935-0.1899-0.0644-0.07750.25110.0935-0.29-0.03030.0887-0.0077-0.01630.1811-0.06870.201215.239-15.94925.356
640.61340.1694-0.02190.60090.0550.60340.04810.3470.0458-0.67690.1258-0.2052-0.51360.10450.04580.8262-0.01730.14510.31090.0170.113152.088.424-25.423
650.31510.0391-0.23720.56760.14910.8240.05070.07080.0326-0.1855-0.0208-0.0508-0.2340.0323-0.01050.15470.0056-0.00450.09530.00640.102844.9791.8411.572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:330 )A1 - 330
2X-RAY DIFFRACTION2( CHAIN A AND RESID 331:618 )A331 - 618
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:69 )B1 - 69
4X-RAY DIFFRACTION4( CHAIN B AND RESID 70:100 )B70 - 100
5X-RAY DIFFRACTION5( CHAIN B AND RESID 101:150 )B101 - 150
6X-RAY DIFFRACTION6( CHAIN B AND RESID 151:280 )B151 - 280
7X-RAY DIFFRACTION7( CHAIN B AND RESID 281:330 )B281 - 330
8X-RAY DIFFRACTION8( CHAIN B AND RESID 331:520 )B331 - 520
9X-RAY DIFFRACTION9( CHAIN B AND RESID 521:563 )B521 - 563
10X-RAY DIFFRACTION10( CHAIN B AND RESID 564:618 )B564 - 618
11X-RAY DIFFRACTION11( CHAIN C AND RESID 1:150 )C1 - 150
12X-RAY DIFFRACTION12( CHAIN C AND RESID 151:330 )C151 - 330
13X-RAY DIFFRACTION13( CHAIN C AND RESID 331:618 )C331 - 618
14X-RAY DIFFRACTION14( CHAIN D AND RESID 2:280 )D2 - 280
15X-RAY DIFFRACTION15( CHAIN D AND RESID 281:618 )D281 - 618
16X-RAY DIFFRACTION16( CHAIN E AND RESID 2:280 )E2 - 280
17X-RAY DIFFRACTION17( CHAIN E AND RESID 281:618 )E281 - 618
18X-RAY DIFFRACTION18( CHAIN F AND RESID 1:205 )F1 - 205
19X-RAY DIFFRACTION19( CHAIN F AND RESID 206:396 )F206 - 396
20X-RAY DIFFRACTION20( CHAIN F AND RESID 397:618 )F397 - 618
21X-RAY DIFFRACTION21( CHAIN G AND RESID 1:205 )G1 - 205
22X-RAY DIFFRACTION22( CHAIN G AND RESID 206:280 )G206 - 280
23X-RAY DIFFRACTION23( CHAIN G AND RESID 281:491 )G281 - 491
24X-RAY DIFFRACTION24( CHAIN G AND RESID 492:618 )G492 - 618
25X-RAY DIFFRACTION25( CHAIN H AND RESID 2:205 )H2 - 205
26X-RAY DIFFRACTION26( CHAIN H AND RESID 206:280 )H206 - 280
27X-RAY DIFFRACTION27( CHAIN H AND RESID 281:330 )H281 - 330
28X-RAY DIFFRACTION28( CHAIN H AND RESID 331:618 )H331 - 618
29X-RAY DIFFRACTION29( CHAIN I AND RESID 1:330 )I1 - 330
30X-RAY DIFFRACTION30( CHAIN I AND RESID 331:618 )I331 - 618
31X-RAY DIFFRACTION31( CHAIN J AND RESID 1:205 )J1 - 205
32X-RAY DIFFRACTION32( CHAIN J AND RESID 206:330 )J206 - 330
33X-RAY DIFFRACTION33( CHAIN J AND RESID 331:618 )J331 - 618
34X-RAY DIFFRACTION34( CHAIN K AND RESID 2:100 )K2 - 100
35X-RAY DIFFRACTION35( CHAIN K AND RESID 101:150 )K101 - 150
36X-RAY DIFFRACTION36( CHAIN K AND RESID 151:280 )K151 - 280
37X-RAY DIFFRACTION37( CHAIN K AND RESID 281:330 )K281 - 330
38X-RAY DIFFRACTION38( CHAIN K AND RESID 331:491 )K331 - 491
39X-RAY DIFFRACTION39( CHAIN K AND RESID 492:587 )K492 - 587
40X-RAY DIFFRACTION40( CHAIN K AND RESID 588:618 )K588 - 618
41X-RAY DIFFRACTION41( CHAIN L AND RESID 2:150 )L2 - 150
42X-RAY DIFFRACTION42( CHAIN L AND RESID 151:280 )L151 - 280
43X-RAY DIFFRACTION43( CHAIN L AND RESID 281:330 )L281 - 330
44X-RAY DIFFRACTION44( CHAIN L AND RESID 331:618 )L331 - 618
45X-RAY DIFFRACTION45( CHAIN M AND RESID 2:69 )M2 - 69
46X-RAY DIFFRACTION46( CHAIN M AND RESID 70:100 )M70 - 100
47X-RAY DIFFRACTION47( CHAIN M AND RESID 101:150 )M101 - 150
48X-RAY DIFFRACTION48( CHAIN M AND RESID 151:205 )M151 - 205
49X-RAY DIFFRACTION49( CHAIN M AND RESID 206:280 )M206 - 280
50X-RAY DIFFRACTION50( CHAIN M AND RESID 281:330 )M281 - 330
51X-RAY DIFFRACTION51( CHAIN M AND RESID 331:491 )M331 - 491
52X-RAY DIFFRACTION52( CHAIN M AND RESID 492:618 )M492 - 618
53X-RAY DIFFRACTION53( CHAIN N AND RESID 2:205 )N2 - 205
54X-RAY DIFFRACTION54( CHAIN N AND RESID 206:330 )N206 - 330
55X-RAY DIFFRACTION55( CHAIN N AND RESID 331:618 )N331 - 618
56X-RAY DIFFRACTION56( CHAIN O AND RESID 2:69 )O2 - 69
57X-RAY DIFFRACTION57( CHAIN O AND RESID 70:100 )O70 - 100
58X-RAY DIFFRACTION58( CHAIN O AND RESID 101:150 )O101 - 150
59X-RAY DIFFRACTION59( CHAIN O AND RESID 151:280 )O151 - 280
60X-RAY DIFFRACTION60( CHAIN O AND RESID 281:330 )O281 - 330
61X-RAY DIFFRACTION61( CHAIN O AND RESID 331:452 )O331 - 452
62X-RAY DIFFRACTION62( CHAIN O AND RESID 453:587 )O453 - 587
63X-RAY DIFFRACTION63( CHAIN O AND RESID 588:618 )O588 - 618
64X-RAY DIFFRACTION64( CHAIN P AND RESID 2:280 )P2 - 280
65X-RAY DIFFRACTION65( CHAIN P AND RESID 281:618 )P281 - 618

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more