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- PDB-6zgp: Crystal structure of the quaternary ammonium Rieske monooxygenase... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6zgp
TitleCrystal structure of the quaternary ammonium Rieske monooxygenase CntA in complex with inhibitor MMV12 (MMV020670)
ComponentsCarnitine monooxygenase oxygenase subunit
KeywordsOXIDOREDUCTASE / Apo / Rieske / Iron-Sulphur Cluster
Function / homology
Function and homology information


carnitine monooxygenase / carnitine metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Carnitine monooxygenase oxygenase subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / Chem-QKQ / Carnitine monooxygenase oxygenase subunit
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsQuareshy, M. / Shanmugam, M. / Bugg, T.D.H. / Cameron, A. / Chen, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2016-307 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition, and intersubunit electron transfer.
Authors: Quareshy, M. / Shanmugam, M. / Townsend, E. / Jameson, E. / Bugg, T.D.H. / Cameron, A.D. / Chen, Y.
History
DepositionJun 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carnitine monooxygenase oxygenase subunit
B: Carnitine monooxygenase oxygenase subunit
C: Carnitine monooxygenase oxygenase subunit
D: Carnitine monooxygenase oxygenase subunit
E: Carnitine monooxygenase oxygenase subunit
F: Carnitine monooxygenase oxygenase subunit
G: Carnitine monooxygenase oxygenase subunit
H: Carnitine monooxygenase oxygenase subunit
I: Carnitine monooxygenase oxygenase subunit
J: Carnitine monooxygenase oxygenase subunit
K: Carnitine monooxygenase oxygenase subunit
L: Carnitine monooxygenase oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)547,65160
Polymers537,36212
Non-polymers10,28948
Water21,7621208
1
A: Carnitine monooxygenase oxygenase subunit
B: Carnitine monooxygenase oxygenase subunit
C: Carnitine monooxygenase oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,91315
Polymers134,3413
Non-polymers2,57212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-67 kcal/mol
Surface area40230 Å2
MethodPISA
2
D: Carnitine monooxygenase oxygenase subunit
E: Carnitine monooxygenase oxygenase subunit
F: Carnitine monooxygenase oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,91315
Polymers134,3413
Non-polymers2,57212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-65 kcal/mol
Surface area41120 Å2
MethodPISA
3
G: Carnitine monooxygenase oxygenase subunit
H: Carnitine monooxygenase oxygenase subunit
I: Carnitine monooxygenase oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,91315
Polymers134,3413
Non-polymers2,57212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-65 kcal/mol
Surface area40820 Å2
MethodPISA
4
J: Carnitine monooxygenase oxygenase subunit
K: Carnitine monooxygenase oxygenase subunit
L: Carnitine monooxygenase oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,91315
Polymers134,3413
Non-polymers2,57212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-66 kcal/mol
Surface area40350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.070, 173.770, 157.290
Angle α, β, γ (deg.)90.000, 90.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 4 or resid 6...
21(chain B and (resid 3 through 4 or resid 6...
31(chain C and (resid 3 through 4 or resid 6...
41(chain D and (resid 3 through 4 or resid 6...
51(chain E and (resid 3 through 4 or resid 6...
61(chain F and (resid 3 through 4 or resid 6...
71(chain G and (resid 3 through 4 or resid 6...
81(chain H and (resid 3 through 4 or resid 6...
91(chain I and (resid 3 through 4 or resid 6...
101(chain J and (resid 3 through 4 or resid 6...
111(chain K and (resid 3 through 4 or resid 6...
121(chain L and (resid 3 through 4 or resid 6...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 4 or resid 6...A3 - 4
121(chain A and (resid 3 through 4 or resid 6...A6 - 29
131(chain A and (resid 3 through 4 or resid 6...A0
141(chain A and (resid 3 through 4 or resid 6...A7
151(chain A and (resid 3 through 4 or resid 6...A10113
161(chain A and (resid 3 through 4 or resid 6...A115 - 12
171(chain A and (resid 3 through 4 or resid 6...A124 - 132
181(chain A and (resid 3 through 4 or resid 6...A135 - 155
191(chain A and (resid 3 through 4 or resid 6...A157 - 169
1101(chain A and (resid 3 through 4 or resid 6...A171 - 179
1111(chain A and (resid 3 through 4 or resid 6...A181 - 21240
1121(chain A and (resid 3 through 4 or resid 6...A25630
1131(chain A and (resid 3 through 4 or resid 6...A232 - 240
1141(chain A and (resid 3 through 4 or resid 6...A256 - 302
1151(chain A and (resid 3 through 4 or resid 6...A350 - 481
1161(chain A and (resid 3 through 4 or resid 6...A501
1171(chain A and (resid 3 through 4 or resid 6...A601
211(chain B and (resid 3 through 4 or resid 6...B3 - 4
221(chain B and (resid 3 through 4 or resid 6...B6 - 29
231(chain B and (resid 3 through 4 or resid 6...B31 - 62
241(chain B and (resid 3 through 4 or resid 6...B108
251(chain B and (resid 3 through 4 or resid 6...B3 - 371
261(chain B and (resid 3 through 4 or resid 6...B2 - 113
271(chain B and (resid 3 through 4 or resid 6...B115 - 122
281(chain B and (resid 3 through 4 or resid 6...B135 - 155
291(chain B and (resid 3 through 4 or resid 6...B181 - 219
2101(chain B and (resid 3 through 4 or resid 6...B181 - 218
2111(chain B and (resid 3 through 4 or resid 6...B220 - 230
2121(chain B and (resid 3 through 4 or resid 6...B256 - 302
2131(chain B and (resid 3 through 4 or resid 6...B304 - 348
2141(chain B and (resid 3 through 4 or resid 6...B350 - 488
2151(chain B and (resid 3 through 4 or resid 6...B350 - 481
2161(chain B and (resid 3 through 4 or resid 6...B501
2171(chain B and (resid 3 through 4 or resid 6...B601
311(chain C and (resid 3 through 4 or resid 6...C3 - 4
321(chain C and (resid 3 through 4 or resid 6...C6 - 29
331(chain C and (resid 3 through 4 or resid 6...C31 - 62
341(chain C and (resid 3 through 4 or resid 6...C108
351(chain C and (resid 3 through 4 or resid 6...C3 - 371
361(chain C and (resid 3 through 4 or resid 6...C2 - 113
371(chain C and (resid 3 through 4 or resid 6...C115 - 122
381(chain C and (resid 3 through 4 or resid 6...C135 - 155
391(chain C and (resid 3 through 4 or resid 6...C181 - 219
3101(chain C and (resid 3 through 4 or resid 6...C181 - 218
3111(chain C and (resid 3 through 4 or resid 6...C220 - 230
3121(chain C and (resid 3 through 4 or resid 6...C256 - 302
3131(chain C and (resid 3 through 4 or resid 6...C304 - 348
3141(chain C and (resid 3 through 4 or resid 6...C350 - 488
3151(chain C and (resid 3 through 4 or resid 6...C350 - 481
3161(chain C and (resid 3 through 4 or resid 6...C501
3171(chain C and (resid 3 through 4 or resid 6...C601
411(chain D and (resid 3 through 4 or resid 6...D3 - 4
421(chain D and (resid 3 through 4 or resid 6...D6 - 29
431(chain D and (resid 3 through 4 or resid 6...D31 - 62
441(chain D and (resid 3 through 4 or resid 6...D108
451(chain D and (resid 3 through 4 or resid 6...D3 - 371
461(chain D and (resid 3 through 4 or resid 6...D2 - 113
471(chain D and (resid 3 through 4 or resid 6...D115 - 122
481(chain D and (resid 3 through 4 or resid 6...D135 - 155
491(chain D and (resid 3 through 4 or resid 6...D181 - 219
4101(chain D and (resid 3 through 4 or resid 6...D181 - 218
4111(chain D and (resid 3 through 4 or resid 6...D220 - 230
4121(chain D and (resid 3 through 4 or resid 6...D256 - 302
4131(chain D and (resid 3 through 4 or resid 6...D304 - 348
4141(chain D and (resid 3 through 4 or resid 6...D350 - 488
4151(chain D and (resid 3 through 4 or resid 6...D350 - 481
4161(chain D and (resid 3 through 4 or resid 6...D501
4171(chain D and (resid 3 through 4 or resid 6...D601
511(chain E and (resid 3 through 4 or resid 6...E3 - 4
521(chain E and (resid 3 through 4 or resid 6...E6 - 29
531(chain E and (resid 3 through 4 or resid 6...E31 - 62
541(chain E and (resid 3 through 4 or resid 6...E108
551(chain E and (resid 3 through 4 or resid 6...E3 - 371
561(chain E and (resid 3 through 4 or resid 6...E2 - 113
571(chain E and (resid 3 through 4 or resid 6...E115 - 122
581(chain E and (resid 3 through 4 or resid 6...E135 - 155
591(chain E and (resid 3 through 4 or resid 6...E181 - 219
5101(chain E and (resid 3 through 4 or resid 6...E181 - 218
5111(chain E and (resid 3 through 4 or resid 6...E220 - 230
5121(chain E and (resid 3 through 4 or resid 6...E256 - 302
5131(chain E and (resid 3 through 4 or resid 6...E304 - 348
5141(chain E and (resid 3 through 4 or resid 6...E350 - 488
5151(chain E and (resid 3 through 4 or resid 6...E350 - 481
5161(chain E and (resid 3 through 4 or resid 6...E501
5171(chain E and (resid 3 through 4 or resid 6...E601
611(chain F and (resid 3 through 4 or resid 6...F3 - 4
621(chain F and (resid 3 through 4 or resid 6...F6 - 29
631(chain F and (resid 3 through 4 or resid 6...F31 - 62
641(chain F and (resid 3 through 4 or resid 6...F108
651(chain F and (resid 3 through 4 or resid 6...F3 - 371
661(chain F and (resid 3 through 4 or resid 6...F2 - 113
671(chain F and (resid 3 through 4 or resid 6...F115 - 122
681(chain F and (resid 3 through 4 or resid 6...F135 - 155
691(chain F and (resid 3 through 4 or resid 6...F181 - 219
6101(chain F and (resid 3 through 4 or resid 6...F181 - 218
6111(chain F and (resid 3 through 4 or resid 6...F220 - 230
6121(chain F and (resid 3 through 4 or resid 6...F256 - 302
6131(chain F and (resid 3 through 4 or resid 6...F304 - 348
6141(chain F and (resid 3 through 4 or resid 6...F350 - 488
6151(chain F and (resid 3 through 4 or resid 6...F350 - 481
6161(chain F and (resid 3 through 4 or resid 6...F501
6171(chain F and (resid 3 through 4 or resid 6...F601
711(chain G and (resid 3 through 4 or resid 6...G3 - 4
721(chain G and (resid 3 through 4 or resid 6...G6 - 29
731(chain G and (resid 3 through 4 or resid 6...G31 - 62
741(chain G and (resid 3 through 4 or resid 6...G108
751(chain G and (resid 3 through 4 or resid 6...G3 - 371
761(chain G and (resid 3 through 4 or resid 6...G2 - 113
771(chain G and (resid 3 through 4 or resid 6...G115 - 122
781(chain G and (resid 3 through 4 or resid 6...G135 - 155
791(chain G and (resid 3 through 4 or resid 6...G181 - 219
7101(chain G and (resid 3 through 4 or resid 6...G181 - 218
7111(chain G and (resid 3 through 4 or resid 6...G220 - 230
7121(chain G and (resid 3 through 4 or resid 6...G256 - 302
7131(chain G and (resid 3 through 4 or resid 6...G304 - 348
7141(chain G and (resid 3 through 4 or resid 6...G350 - 488
7151(chain G and (resid 3 through 4 or resid 6...G350 - 481
7161(chain G and (resid 3 through 4 or resid 6...G501
7171(chain G and (resid 3 through 4 or resid 6...G601
811(chain H and (resid 3 through 4 or resid 6...H3 - 4
821(chain H and (resid 3 through 4 or resid 6...H6 - 29
831(chain H and (resid 3 through 4 or resid 6...H31 - 62
841(chain H and (resid 3 through 4 or resid 6...H108
851(chain H and (resid 3 through 4 or resid 6...H3 - 371
861(chain H and (resid 3 through 4 or resid 6...H2 - 113
871(chain H and (resid 3 through 4 or resid 6...H115 - 122
881(chain H and (resid 3 through 4 or resid 6...H135 - 155
891(chain H and (resid 3 through 4 or resid 6...H181 - 219
8101(chain H and (resid 3 through 4 or resid 6...H181 - 218
8111(chain H and (resid 3 through 4 or resid 6...H220 - 230
8121(chain H and (resid 3 through 4 or resid 6...H256 - 302
8131(chain H and (resid 3 through 4 or resid 6...H304 - 348
8141(chain H and (resid 3 through 4 or resid 6...H350 - 488
8151(chain H and (resid 3 through 4 or resid 6...H350 - 481
8161(chain H and (resid 3 through 4 or resid 6...H501
8171(chain H and (resid 3 through 4 or resid 6...H601
911(chain I and (resid 3 through 4 or resid 6...I3 - 4
921(chain I and (resid 3 through 4 or resid 6...I6 - 29
931(chain I and (resid 3 through 4 or resid 6...I31 - 62
941(chain I and (resid 3 through 4 or resid 6...I108
951(chain I and (resid 3 through 4 or resid 6...I3 - 371
961(chain I and (resid 3 through 4 or resid 6...I2 - 113
971(chain I and (resid 3 through 4 or resid 6...I115 - 122
981(chain I and (resid 3 through 4 or resid 6...I135 - 155
991(chain I and (resid 3 through 4 or resid 6...I181 - 219
9101(chain I and (resid 3 through 4 or resid 6...I181 - 218
9111(chain I and (resid 3 through 4 or resid 6...I220 - 230
9121(chain I and (resid 3 through 4 or resid 6...I256 - 302
9131(chain I and (resid 3 through 4 or resid 6...I304 - 348
9141(chain I and (resid 3 through 4 or resid 6...I350 - 488
9151(chain I and (resid 3 through 4 or resid 6...I350 - 481
9161(chain I and (resid 3 through 4 or resid 6...I501
9171(chain I and (resid 3 through 4 or resid 6...I601
1011(chain J and (resid 3 through 4 or resid 6...J3 - 4
1021(chain J and (resid 3 through 4 or resid 6...J6 - 29
1031(chain J and (resid 3 through 4 or resid 6...J31 - 62
1041(chain J and (resid 3 through 4 or resid 6...J108
1051(chain J and (resid 3 through 4 or resid 6...J3 - 371
1061(chain J and (resid 3 through 4 or resid 6...J2 - 113
1071(chain J and (resid 3 through 4 or resid 6...J115 - 122
1081(chain J and (resid 3 through 4 or resid 6...J135 - 155
1091(chain J and (resid 3 through 4 or resid 6...J181 - 219
10101(chain J and (resid 3 through 4 or resid 6...J181 - 218
10111(chain J and (resid 3 through 4 or resid 6...J220 - 230
10121(chain J and (resid 3 through 4 or resid 6...J256 - 302
10131(chain J and (resid 3 through 4 or resid 6...J304 - 348
10141(chain J and (resid 3 through 4 or resid 6...J350 - 488
10151(chain J and (resid 3 through 4 or resid 6...J350 - 481
10161(chain J and (resid 3 through 4 or resid 6...J501
10171(chain J and (resid 3 through 4 or resid 6...J601
1111(chain K and (resid 3 through 4 or resid 6...K3 - 4
1121(chain K and (resid 3 through 4 or resid 6...K6 - 29
1131(chain K and (resid 3 through 4 or resid 6...K31 - 62
1141(chain K and (resid 3 through 4 or resid 6...K108
1151(chain K and (resid 3 through 4 or resid 6...K3 - 371
1161(chain K and (resid 3 through 4 or resid 6...K2 - 113
1171(chain K and (resid 3 through 4 or resid 6...K115 - 122
1181(chain K and (resid 3 through 4 or resid 6...K135 - 155
1191(chain K and (resid 3 through 4 or resid 6...K181 - 219
11101(chain K and (resid 3 through 4 or resid 6...K181 - 218
11111(chain K and (resid 3 through 4 or resid 6...K220 - 230
11121(chain K and (resid 3 through 4 or resid 6...K256 - 302
11131(chain K and (resid 3 through 4 or resid 6...K304 - 348
11141(chain K and (resid 3 through 4 or resid 6...K350 - 488
11151(chain K and (resid 3 through 4 or resid 6...K350 - 481
11161(chain K and (resid 3 through 4 or resid 6...K501
11171(chain K and (resid 3 through 4 or resid 6...K601
1211(chain L and (resid 3 through 4 or resid 6...L3 - 4
1221(chain L and (resid 3 through 4 or resid 6...L6 - 29
1231(chain L and (resid 3 through 4 or resid 6...L31 - 62
1241(chain L and (resid 3 through 4 or resid 6...L108
1251(chain L and (resid 3 through 4 or resid 6...L3 - 371
1261(chain L and (resid 3 through 4 or resid 6...L2 - 113
1271(chain L and (resid 3 through 4 or resid 6...L115 - 122
1281(chain L and (resid 3 through 4 or resid 6...L135 - 155
1291(chain L and (resid 3 through 4 or resid 6...L181 - 219
12101(chain L and (resid 3 through 4 or resid 6...L181 - 218
12111(chain L and (resid 3 through 4 or resid 6...L220 - 230
12121(chain L and (resid 3 through 4 or resid 6...L256 - 302
12131(chain L and (resid 3 through 4 or resid 6...L304 - 348
12141(chain L and (resid 3 through 4 or resid 6...L350 - 488
12151(chain L and (resid 3 through 4 or resid 6...L350 - 481
12161(chain L and (resid 3 through 4 or resid 6...L501
12171(chain L and (resid 3 through 4 or resid 6...L601

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Carnitine monooxygenase oxygenase subunit / Carnitine monooxygenase alpha subunit


Mass: 44780.172 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_01970, ...Gene: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_01970, DOL94_04925, DVA79_16365, E2533_13315, E2536_16135, E5294_15630, E5979_13670, EA685_07170, EA686_01565, EA706_03020, EA722_03860, EA746_003300, EWO92_12480, EWO96_16565, EWP49_15025, FD887_09300, FD913_14110, FJU36_15000, FJU42_16200, FJU76_14830, FJU79_08840, FJU87_10695, FJV14_20515, LV38_02893, NCTC13305_01609, SAMEA104305283_02985, SAMEA104305351_01970
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A059ZPP5, carnitine monooxygenase

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Non-polymers , 5 types, 1256 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-QKQ / ~{N}-(3-imidazol-1-ylpropyl)-8-(4-methoxyphenyl)-1,6-naphthyridine-2-carboxamide


Mass: 387.434 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C22H21N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 10mM HEPES, 20% PEG3350 (w/v) 0.2M NaSCN, 0.5mM TCEP, 250mM MMV020670
PH range: 7.0 - 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 2.01→80.67 Å / Num. obs: 322879 / % possible obs: 99.44 % / Redundancy: 6.9 % / Biso Wilson estimate: 33.1 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.06784 / Rrim(I) all: 0.1787 / Net I/σ(I): 6.88
Reflection shellResolution: 2.01→2.082 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.783 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 32095 / CC1/2: 0.698 / CC star: 0.907 / Rpim(I) all: 0.7328 / Rrim(I) all: 1.929 / % possible all: 99.07

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y9D

6y9d


Resolution: 2.01→80.663 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 16241 5.04 %
Rwork0.2139 305750 -
obs0.2159 321991 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.25 Å2 / Biso mean: 51.6225 Å2 / Biso min: 18.93 Å2
Refinement stepCycle: final / Resolution: 2.01→80.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34907 0 792 1208 36907
Biso mean--65.4 44.18 -
Num. residues----4305
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12180X-RAY DIFFRACTION3.966TORSIONAL
12B12180X-RAY DIFFRACTION3.966TORSIONAL
13C12180X-RAY DIFFRACTION3.966TORSIONAL
14D12180X-RAY DIFFRACTION3.966TORSIONAL
15E12180X-RAY DIFFRACTION3.966TORSIONAL
16F12180X-RAY DIFFRACTION3.966TORSIONAL
17G12180X-RAY DIFFRACTION3.966TORSIONAL
18H12180X-RAY DIFFRACTION3.966TORSIONAL
19I12180X-RAY DIFFRACTION3.966TORSIONAL
110J12180X-RAY DIFFRACTION3.966TORSIONAL
111K12180X-RAY DIFFRACTION3.966TORSIONAL
112L12180X-RAY DIFFRACTION3.966TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.01-2.03280.41955120.39471016399
2.0328-2.05680.41985330.37511009799
2.0568-2.08180.39964590.37041020999
2.0818-2.10820.39275470.3561018599
2.1082-2.13590.37015330.32581012299
2.1359-2.16520.36315190.3121022099
2.1652-2.19610.34285210.30321010399
2.1961-2.22890.34496350.29921012899
2.2289-2.26380.35165600.292510141100
2.2638-2.30090.30835680.28410119100
2.3009-2.34050.3295570.27321020599
2.3405-2.38310.30825010.26431014699
2.3831-2.42890.28595340.25691017999
2.4289-2.47850.29144510.2531027599
2.4785-2.53240.32025180.251110251100
2.5324-2.59130.30324990.244910262100
2.5913-2.65610.30515390.23641011799
2.6561-2.7280.27975290.222610225100
2.728-2.80820.25865430.219510209100
2.8082-2.89890.27985600.230810206100
2.8989-3.00250.2795900.229410173100
3.0025-3.12270.26885630.220410200100
3.1227-3.26480.25255860.202310200100
3.2648-3.4370.24485140.206810244100
3.437-3.65230.23885400.192310215100
3.6523-3.93430.21135660.171410252100
3.9343-4.33020.19756090.150910183100
4.3302-4.95670.17815720.147210175100
4.9567-6.24460.20485400.166710295100
6.2446-80.60.20285430.18041025198
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)
10.7599-0.00460.39740.30190.24021.2606-0.02450.0117-0.06860.0077-0.06180.1215-0.0319-0.33310.00010.25480.0098-0.0040.42010.01650.35167.993518.258335.5097
20.15150.06060.14050.02130.04260.1385-0.36970.07810.6245-0.0996-0.2790.6996-0.67690.07180.00771.0580.0349-0.01041.3192-0.19530.6346-1.271130.741163.5698
30.9951-0.58260.97870.9523-0.3444.2917-0.2092-0.4390.06430.4318-0.02630.7016-0.7611-0.3753-0.84060.27390.00340.25261.1382-0.10070.5065-10.266526.724755.0318
40.65840.03640.42140.45620.07671.5794-0.1287-0.3297-0.00970.1707-0.03630.0911-0.2401-0.5838-0.00010.42640.06330.04730.5629-0.04210.3674.208924.697853.6165
50.6428-0.3662-0.2970.048-0.00481.3347-0.0097-0.04520.1169-0.01790.0351-0.05270.09190.527-0.00280.27590.01740.04480.4812-0.01630.34352.838614.124338.3563
60.52480.48090.20190.23870.25730.3737-0.17050.43530.1808-0.05130.07830.0777-0.0713-0.1413-0.00010.32370.00380.0410.64230.12260.41443.36222.322817.9396
70.876-0.41460.05760.44020.42540.86840.04030.42610.1363-0.14630.0289-0.0631-0.0817-0.034-0.00020.3340.01740.07910.35130.04270.395837.570721.117725.1724
80.7342-0.07510.313-0.15220.0271.87580.046-0.0799-0.01080.1813-0.0077-0.03230.1456-0.2704-0.0040.50830.00020.04330.4213-0.00620.283226.810816.705376.3031
90.1853-0.04780.09390.18980.34150.56080.11760.13860.0160.10280.0609-0.12790.06250.77570.00070.4747-0.0085-0.0220.7102-0.05360.333950.345620.57676.1345
100.37140.3202-0.13650.46910.26920.8730.0575-0.0589-0.01990.14220.04460.06760.02320.52690.00040.45210.03740.00810.5013-0.04930.294747.663520.136468.7261
111.3487-0.06470.3087-0.08740.01821.1762-0.0205-0.0416-0.01710.0423-0.0314-0.00590.07290.25260.00020.29920.0289-0.01680.29740.00620.344737.2689-70.585643.0408
120.17370.087-0.05080.22910.28230.2948-0.04060.4987-0.1275-0.0920.1584-0.1088-0.36640.55210.00450.4393-0.05350.00960.97290.00230.348153.196-63.470120.2853
130.98120.08690.69890.09190.09261.2965-0.07490.37870.070.0344-0.04940.0734-0.18680.3929-0.00060.292-0.0004-0.00720.4210.06670.319141.7314-65.164124.5088
141.34740.02690.3381-0.0357-0.04160.8675-0.0111-0.27520.04440.03560.0569-0.00510.0341-0.2623-0.00010.2768-0.00980.03430.40450.03110.3255-6.8036-70.010741.3687
150.2159-0.31660.22380.4077-0.28420.1697-0.3226-0.44550.18030.27480.5402-0.0216-0.39030.13540.02590.58320.00320.02950.8412-0.09920.45542.9526-61.282967.2448
160.7490.07110.16010.0957-0.230.8923-0.0313-0.45370.18210.02080.0773-0.0889-0.1526-0.1125-0.00010.33660.03340.03380.4961-0.07970.39232.8214-58.777151.5374
170.21830.01320.0750.2984-0.06810.07530.1146-0.6527-0.1130.017-0.0252-0.04780.1515-0.2014-0.00090.3804-0.05460.01340.67070.09020.374412.132-77.227659.0969
180.8698-0.39820.1328-0.22370.08021.50280.02130.2342-0.0245-0.0707-0.01880.04820.15720.3772-0.00330.27960.03450.0060.2363-0.03080.287118.4533-71.70871.9726
190.40290.0330.14990.405-0.34190.66820.02170.1287-0.00590.07540.09010.10870.0397-0.44390.00150.2678-0.00520.01260.38140.02030.3288-6.0134-63.16873.2958
200.2692-0.1316-0.12270.2798-0.12230.90910.03860.072-0.03960.0841-0.02860.00140.0307-0.17650.00010.2557-0.02370.00030.1932-0.02120.2826-1.0524-64.79818.4196
210.67960.06770.0897-0.05220.00121.46480.0187-0.17070.01480.0695-0.0101-0.0167-0.08920.1359-0.00140.2310.0057-0.01740.2938-0.0260.2666-14.0634-21.250753.755
220.5713-0.2648-0.20440.023-0.03130.52090.15560.07050.0541-0.01780.06950.0642-0.1913-0.8650.0870.2211-0.0026-0.04150.6830.01380.2843-40.4261-26.481451.6165
231.0456-0.9025-0.26280.66390.23380.9035-0.21510.15-0.2607-0.22460.32360.38980.4108-0.93180.01480.282-0.1236-0.00910.56850.02940.3872-33.7426-31.023255.7654
240.01390.04630.430.4683-0.12681.43960.0557-0.07710.0135-0.0707-0.0049-0.01590.1432-0.44050.00370.2431-0.0111-0.02920.3555-0.01170.2852-34.3875-27.112946.0787
250.77190.0457-0.1824-0.0253-0.03840.99580.0279-0.05590.0631-0.02410.0052-0.03030.0180.30590.00060.2211-0.0361-0.00490.258-0.00310.28325.3203-20.778212.9792
260.2847-0.1055-0.15290.2610.27750.22790.1277-0.1559-0.00320.0890.0665-0.02470.24030.4810.02550.3070.0758-0.05850.7928-0.04840.313120.8769-28.522535.5027
270.54830.137-0.38490.18580.06141.312-0.0183-0.3470.03670.067-0.02130.06290.15830.3828-0.00140.24890.0283-0.0190.37850.01370.26859.6362-26.870131.2655
281.4980.052-0.6474-0.075-0.18361.1139-0.05210.10160.027-0.01830.04060.0065-0.1321-0.43540.00060.21430.0195-0.03320.37020.02260.2917-40.6902-21.255716.1479
290.38350.3751-0.0030.4137-0.38890.6096-0.2220.97280.0533-0.20970.1007-0.1330.2199-0.1983-0.00760.3152-0.09830.02270.6662-0.02930.2871-28.447-27.257-5.5429
300.4257-0.1834-0.29960.1529-0.11060.6549-0.08460.0665-0.20140.0642-0.04790.02150.2039-0.2368-0.00020.3039-0.08350.04630.2603-0.04510.3595-31.5082-36.36726.3996
310.46870.014-0.02790.4287-0.07080.2018-0.11350.7387-0.00790.07950.0166-0.0744-0.0875-0.21590.00160.2886-0.0014-0.02550.26290.11850.3612-18.8975-18.33830.2637
320.8785-0.17720.29870.0376-0.20411.69010.0245-0.05780.00610.13050.03-0.0133-0.16570.2167-0.00050.3369-0.0291-0.00470.22850.00320.286931.3785-20.9592132.3687
330.3303-0.3135-0.16210.2811-0.06430.50750.0391-0.1031-0.054-0.00850.06530.1656-0.1482-0.94710.01410.272-0.03980.0070.76690.07120.33164.9716-24.2334132.0295
340.45770.09320.54740.3276-0.25741.53140.0817-0.0127-0.05450.00480.049-0.01850.0626-0.32440.00040.2989-0.02-0.00620.30360.02930.294111.8916-25.3191126.4541
350.17070.2795-0.06610.3615-0.47080.88580.06550.02190.04530.0399-0.2330.0866-0.13270.5509-0.03070.3068-0.09530.01350.6662-0.01540.297251.598-19.484698.5933
360.4014-0.0697-0.27720.1773-0.1840.2691-0.03620.2761-0.02840.01090.0072-0.01120.1170.0937-00.3159-0.02060.02440.6358-0.00030.324540.5458-23.527774.4264
370.13130.14180.16140.59830.01390.4594-0.0456-0.26160.1728-0.239-0.2323-0.01050.22221.0271-0.31760.19190.05860.08231.06380.0630.281158.7741-26.311998.123
380.7832-0.5647-1.27930.42880.92862.0765-0.4567-0.0083-0.49750.1959-0.25310.00860.71170.0798-0.19790.45660.0636-0.01361.46380.09080.528962.9613-32.4061118.853
391.35230.1428-0.08480.45990.07930.71280.1436-0.3779-0.0269-0.04180.2969-0.52960.22130.65521.46720.19780.0691-0.06631.67850.08240.41467.9535-31.3245110.3234
400.44220.30490.11420.4191-0.10220.3867-0.1268-0.2734-0.0048-0.01570.04380.00590.26040.8975-0.04280.3580.20040.03570.7860.03040.257355.2438-33.5932101.9396
410.1667-0.06940.06790.2047-0.02730.3003-0.0479-0.18440.2127-0.02180.0548-0.33930.30450.3794-0.00140.4740.09840.06560.54510.04250.314949.2457-37.4998111.7203
420.6595-0.3237-0.19660.7721-0.24380.34170.1452-0.24570.20360.38370.11380.081-0.73421.33010.23780.1631-0.3367-0.12251.2931-0.08810.330357.3162-16.4908117.9862
430.5742-0.1341-0.17880.0328-0.06441.33030.03820.0567-0.0153-0.01830.07890.0538-0.0992-0.35070.00010.278-0.0238-0.04450.50160.08740.33194.9673-19.278694.7083
441.09420.4926-0.18950.6166-0.37690.9099-0.06750.4178-0.1645-0.15570.1107-0.06630.08870.05020.00120.3071-0.0431-0.0250.5071-0.03280.326918.9083-26.320477.9226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 204 )A3 - 204
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 221 )A205 - 221
3X-RAY DIFFRACTION3chain 'A' and (resid 222 through 263 )A222 - 263
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 371 )A264 - 371
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 203 )B3 - 203
6X-RAY DIFFRACTION6chain 'B' and (resid 204 through 287 )B204 - 287
7X-RAY DIFFRACTION7chain 'B' and (resid 288 through 371 )B288 - 371
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 192 )C3 - 192
9X-RAY DIFFRACTION9chain 'C' and (resid 193 through 287 )C193 - 287
10X-RAY DIFFRACTION10chain 'C' and (resid 288 through 371 )C288 - 371
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 203 )D3 - 203
12X-RAY DIFFRACTION12chain 'D' and (resid 204 through 263 )D204 - 263
13X-RAY DIFFRACTION13chain 'D' and (resid 264 through 371 )D264 - 371
14X-RAY DIFFRACTION14chain 'E' and (resid 3 through 212 )E3 - 212
15X-RAY DIFFRACTION15chain 'E' and (resid 213 through 256 )E213 - 256
16X-RAY DIFFRACTION16chain 'E' and (resid 257 through 335 )E257 - 335
17X-RAY DIFFRACTION17chain 'E' and (resid 336 through 371 )E336 - 371
18X-RAY DIFFRACTION18chain 'F' and (resid 3 through 182 )F3 - 182
19X-RAY DIFFRACTION19chain 'F' and (resid 183 through 263 )F183 - 263
20X-RAY DIFFRACTION20chain 'F' and (resid 264 through 371 )F264 - 371
21X-RAY DIFFRACTION21chain 'G' and (resid 3 through 192 )G3 - 192
22X-RAY DIFFRACTION22chain 'G' and (resid 193 through 240 )G193 - 240
23X-RAY DIFFRACTION23chain 'G' and (resid 241 through 287 )G241 - 287
24X-RAY DIFFRACTION24chain 'G' and (resid 288 through 371 )G288 - 371
25X-RAY DIFFRACTION25chain 'H' and (resid 3 through 203 )H3 - 203
26X-RAY DIFFRACTION26chain 'H' and (resid 204 through 263 )H204 - 263
27X-RAY DIFFRACTION27chain 'H' and (resid 264 through 371 )H264 - 371
28X-RAY DIFFRACTION28chain 'I' and (resid 3 through 192 )I3 - 192
29X-RAY DIFFRACTION29chain 'I' and (resid 193 through 277 )I193 - 277
30X-RAY DIFFRACTION30chain 'I' and (resid 278 through 318 )I278 - 318
31X-RAY DIFFRACTION31chain 'I' and (resid 319 through 371 )I319 - 371
32X-RAY DIFFRACTION32chain 'J' and (resid 3 through 192 )J3 - 192
33X-RAY DIFFRACTION33chain 'J' and (resid 193 through 263 )J193 - 263
34X-RAY DIFFRACTION34chain 'J' and (resid 264 through 371 )J264 - 371
35X-RAY DIFFRACTION35chain 'K' and (resid 3 through 83 )K3 - 83
36X-RAY DIFFRACTION36chain 'K' and (resid 84 through 141 )K84 - 141
37X-RAY DIFFRACTION37chain 'K' and (resid 142 through 203 )K142 - 203
38X-RAY DIFFRACTION38chain 'K' and (resid 204 through 229 )K204 - 229
39X-RAY DIFFRACTION39chain 'K' and (resid 230 through 263 )K230 - 263
40X-RAY DIFFRACTION40chain 'K' and (resid 264 through 305 )K264 - 305
41X-RAY DIFFRACTION41chain 'K' and (resid 306 through 335 )K306 - 335
42X-RAY DIFFRACTION42chain 'K' and (resid 336 through 371 )K336 - 371
43X-RAY DIFFRACTION43chain 'L' and (resid 3 through 192 )L3 - 192
44X-RAY DIFFRACTION44chain 'L' and (resid 193 through 371 )L193 - 371

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