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- PDB-6pam: Structure of a bacterial Atm1-family ABC transporter with MgADP bound -

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Basic information

Entry
Database: PDB / ID: 6pam
TitleStructure of a bacterial Atm1-family ABC transporter with MgADP bound
ComponentsATM1-type heavy metal exporter
KeywordsTRANSPORT PROTEIN / ABC transporter / ABC exporter / ATPase / membrane protein
Function / homology
Function and homology information


Translocases / response to mercury ion / ABC-type transporter activity / monoatomic ion transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATM1-type heavy metal exporter
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsFan, C. / Kaiser, J.T. / Rees, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: A structural framework for unidirectional transport by a bacterial ABC exporter.
Authors: Chengcheng Fan / Jens T Kaiser / Douglas C Rees /
Abstract: The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from (Atm1) can export glutathione derivatives and confer ...The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from (Atm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying the Atm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As Atm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport by Atm1. One of the disulfide crosslinked Atm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.
History
DepositionJun 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_label_asym_id
Revision 1.2Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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: ATM1-type heavy metal exporter
B: ATM1-type heavy metal exporter
C: ATM1-type heavy metal exporter
D: ATM1-type heavy metal exporter
E: ATM1-type heavy metal exporter
F: ATM1-type heavy metal exporter
G: ATM1-type heavy metal exporter
H: ATM1-type heavy metal exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)546,04124
Polymers542,4298
Non-polymers3,61216
Water0
1
A: ATM1-type heavy metal exporter
B: ATM1-type heavy metal exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,5106
Polymers135,6072
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14280 Å2
ΔGint-110 kcal/mol
Surface area53320 Å2
MethodPISA
2
C: ATM1-type heavy metal exporter
D: ATM1-type heavy metal exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,5106
Polymers135,6072
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-112 kcal/mol
Surface area52810 Å2
MethodPISA
3
E: ATM1-type heavy metal exporter
F: ATM1-type heavy metal exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,5106
Polymers135,6072
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14670 Å2
ΔGint-109 kcal/mol
Surface area54230 Å2
MethodPISA
4
G: ATM1-type heavy metal exporter
H: ATM1-type heavy metal exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,5106
Polymers135,6072
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14380 Å2
ΔGint-115 kcal/mol
Surface area53540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.180, 133.610, 134.260
Angle α, β, γ (deg.)110.620, 98.280, 101.200
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 16 or resid 19 through 20...
21(chain B and (resid 16 or resid 19 through 20...
31(chain C and (resid 16 or resid 19 through 20...
41(chain D and (resid 16 or resid 19 through 20...
51(chain E and (resid 16 or resid 19 through 20...
61(chain F and (resid 16 or resid 19 through 20...
12(chain G and (resid 14 through 73 or resid 75...
22(chain H and (resid 14 through 73 or resid 75...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 16 or resid 19 through 20...A16
121(chain A and (resid 16 or resid 19 through 20...A19 - 20
131(chain A and (resid 16 or resid 19 through 20...A22 - 27
141(chain A and (resid 16 or resid 19 through 20...A38 - 72
151(chain A and (resid 16 or resid 19 through 20...A75
161(chain A and (resid 16 or resid 19 through 20...A8 - 126
171(chain A and (resid 16 or resid 19 through 20...A134
181(chain A and (resid 16 or resid 19 through 20...A140
191(chain A and (resid 16 or resid 19 through 20...A142
1101(chain A and (resid 16 or resid 19 through 20...A42
1111(chain A and (resid 16 or resid 19 through 20...A1 - 148
1121(chain A and (resid 16 or resid 19 through 20...A150 - 159
1131(chain A and (resid 16 or resid 19 through 20...A0
1141(chain A and (resid 16 or resid 19 through 20...A185
1151(chain A and (resid 16 or resid 19 through 20...A13 - 702
1161(chain A and (resid 16 or resid 19 through 20...A335 - 341
1171(chain A and (resid 16 or resid 19 through 20...A13 - 702
1181(chain A and (resid 16 or resid 19 through 20...A349 - 357
1191(chain A and (resid 16 or resid 19 through 20...A13 - 702
1201(chain A and (resid 16 or resid 19 through 20...A384 - 420
1211(chain A and (resid 16 or resid 19 through 20...A13 - 702
1221(chain A and (resid 16 or resid 19 through 20...A422 - 463
1231(chain A and (resid 16 or resid 19 through 20...A0
1241(chain A and (resid 16 or resid 19 through 20...A491 - 493
1251(chain A and (resid 16 or resid 19 through 20...A532 - 580
1261(chain A and (resid 16 or resid 19 through 20...A532 - 584
1271(chain A and (resid 16 or resid 19 through 20...A586 - 598
211(chain B and (resid 16 or resid 19 through 20...B16
221(chain B and (resid 16 or resid 19 through 20...B19 - 20
231(chain B and (resid 16 or resid 19 through 20...B22 - 27
241(chain B and (resid 16 or resid 19 through 20...B29
251(chain B and (resid 16 or resid 19 through 20...B33 - 34
261(chain B and (resid 16 or resid 19 through 20...B38 - 72
271(chain B and (resid 16 or resid 19 through 20...B75 - 106
281(chain B and (resid 16 or resid 19 through 20...B108 - 126
291(chain B and (resid 16 or resid 19 through 20...B134
2101(chain B and (resid 16 or resid 19 through 20...B138
2111(chain B and (resid 16 or resid 19 through 20...B140
2121(chain B and (resid 16 or resid 19 through 20...B142
2131(chain B and (resid 16 or resid 19 through 20...B147 - 1159
2141(chain B and (resid 16 or resid 19 through 20...B161 - 179
2151(chain B and (resid 16 or resid 19 through 20...B18 - 179
2161(chain B and (resid 16 or resid 19 through 20...B181 - 245
2171(chain B and (resid 16 or resid 19 through 20...B247 - 259
2181(chain B and (resid 16 or resid 19 through 20...B261 - 333
2191(chain B and (resid 16 or resid 19 through 20...B335 - 341
2201(chain B and (resid 16 or resid 19 through 20...B344
2211(chain B and (resid 16 or resid 19 through 20...B384 - 420
2221(chain B and (resid 16 or resid 19 through 20...B422 - 463
2231(chain B and (resid 16 or resid 19 through 20...B465 - 471
2241(chain B and (resid 16 or resid 19 through 20...B473 - 489
2251(chain B and (resid 16 or resid 19 through 20...B491 - 493
2261(chain B and (resid 16 or resid 19 through 20...B495 - 530
2271(chain B and (resid 16 or resid 19 through 20...B532 - 584
2281(chain B and (resid 16 or resid 19 through 20...B586 - 598
311(chain C and (resid 16 or resid 19 through 20...C16
321(chain C and (resid 16 or resid 19 through 20...C19 - 20
331(chain C and (resid 16 or resid 19 through 20...C22 - 27
341(chain C and (resid 16 or resid 19 through 20...C29
351(chain C and (resid 16 or resid 19 through 20...C33 - 34
361(chain C and (resid 16 or resid 19 through 20...C38 - 72
371(chain C and (resid 16 or resid 19 through 20...C75 - 106
381(chain C and (resid 16 or resid 19 through 20...C108 - 126
391(chain C and (resid 16 or resid 19 through 20...C134
3101(chain C and (resid 16 or resid 19 through 20...C138
3111(chain C and (resid 16 or resid 19 through 20...C140
3121(chain C and (resid 16 or resid 19 through 20...C142
3131(chain C and (resid 16 or resid 19 through 20...C147 - 1159
3141(chain C and (resid 16 or resid 19 through 20...C161 - 179
3151(chain C and (resid 16 or resid 19 through 20...C18 - 179
3161(chain C and (resid 16 or resid 19 through 20...C181 - 245
3171(chain C and (resid 16 or resid 19 through 20...C247 - 259
3181(chain C and (resid 16 or resid 19 through 20...C261 - 333
3191(chain C and (resid 16 or resid 19 through 20...C335 - 341
3201(chain C and (resid 16 or resid 19 through 20...C344
3211(chain C and (resid 16 or resid 19 through 20...C384 - 420
3221(chain C and (resid 16 or resid 19 through 20...C422 - 463
3231(chain C and (resid 16 or resid 19 through 20...C465 - 471
3241(chain C and (resid 16 or resid 19 through 20...C473 - 489
3251(chain C and (resid 16 or resid 19 through 20...C491 - 493
3261(chain C and (resid 16 or resid 19 through 20...C495 - 530
3271(chain C and (resid 16 or resid 19 through 20...C532 - 584
3281(chain C and (resid 16 or resid 19 through 20...C586 - 598
411(chain D and (resid 16 or resid 19 through 20...D16
421(chain D and (resid 16 or resid 19 through 20...D19 - 20
431(chain D and (resid 16 or resid 19 through 20...D22 - 27
441(chain D and (resid 16 or resid 19 through 20...D29
451(chain D and (resid 16 or resid 19 through 20...D33 - 34
461(chain D and (resid 16 or resid 19 through 20...D38 - 72
471(chain D and (resid 16 or resid 19 through 20...D75 - 106
481(chain D and (resid 16 or resid 19 through 20...D108 - 126
491(chain D and (resid 16 or resid 19 through 20...D134
4101(chain D and (resid 16 or resid 19 through 20...D138
4111(chain D and (resid 16 or resid 19 through 20...D140
4121(chain D and (resid 16 or resid 19 through 20...D142
4131(chain D and (resid 16 or resid 19 through 20...D147 - 1159
4141(chain D and (resid 16 or resid 19 through 20...D161 - 179
4151(chain D and (resid 16 or resid 19 through 20...D18 - 179
4161(chain D and (resid 16 or resid 19 through 20...D181 - 245
4171(chain D and (resid 16 or resid 19 through 20...D247 - 259
4181(chain D and (resid 16 or resid 19 through 20...D261 - 333
4191(chain D and (resid 16 or resid 19 through 20...D335 - 341
4201(chain D and (resid 16 or resid 19 through 20...D344
4211(chain D and (resid 16 or resid 19 through 20...D384 - 420
4221(chain D and (resid 16 or resid 19 through 20...D422 - 463
4231(chain D and (resid 16 or resid 19 through 20...D465 - 471
4241(chain D and (resid 16 or resid 19 through 20...D473 - 489
4251(chain D and (resid 16 or resid 19 through 20...D491 - 493
4261(chain D and (resid 16 or resid 19 through 20...D495 - 530
4271(chain D and (resid 16 or resid 19 through 20...D532 - 584
4281(chain D and (resid 16 or resid 19 through 20...D586 - 598
511(chain E and (resid 16 or resid 19 through 20...E16
521(chain E and (resid 16 or resid 19 through 20...E19 - 20
531(chain E and (resid 16 or resid 19 through 20...E22 - 27
541(chain E and (resid 16 or resid 19 through 20...E29
551(chain E and (resid 16 or resid 19 through 20...E33 - 34
561(chain E and (resid 16 or resid 19 through 20...E38 - 72
571(chain E and (resid 16 or resid 19 through 20...E75 - 106
581(chain E and (resid 16 or resid 19 through 20...E108 - 126
591(chain E and (resid 16 or resid 19 through 20...E134
5101(chain E and (resid 16 or resid 19 through 20...E138
5111(chain E and (resid 16 or resid 19 through 20...E140
5121(chain E and (resid 16 or resid 19 through 20...E142
5131(chain E and (resid 16 or resid 19 through 20...E147 - 1159
5141(chain E and (resid 16 or resid 19 through 20...E161 - 179
5151(chain E and (resid 16 or resid 19 through 20...E18 - 179
5161(chain E and (resid 16 or resid 19 through 20...E181 - 245
5171(chain E and (resid 16 or resid 19 through 20...E247 - 259
5181(chain E and (resid 16 or resid 19 through 20...E261 - 333
5191(chain E and (resid 16 or resid 19 through 20...E335 - 341
5201(chain E and (resid 16 or resid 19 through 20...E344
5211(chain E and (resid 16 or resid 19 through 20...E384 - 420
5221(chain E and (resid 16 or resid 19 through 20...E422 - 463
5231(chain E and (resid 16 or resid 19 through 20...E465 - 471
5241(chain E and (resid 16 or resid 19 through 20...E473 - 489
5251(chain E and (resid 16 or resid 19 through 20...E491 - 493
5261(chain E and (resid 16 or resid 19 through 20...E495 - 530
5271(chain E and (resid 16 or resid 19 through 20...E532 - 584
5281(chain E and (resid 16 or resid 19 through 20...E586 - 598
611(chain F and (resid 16 or resid 19 through 20...F16
621(chain F and (resid 16 or resid 19 through 20...F19 - 20
631(chain F and (resid 16 or resid 19 through 20...F22 - 27
641(chain F and (resid 16 or resid 19 through 20...F29
651(chain F and (resid 16 or resid 19 through 20...F33 - 34
661(chain F and (resid 16 or resid 19 through 20...F38 - 72
671(chain F and (resid 16 or resid 19 through 20...F75 - 106
681(chain F and (resid 16 or resid 19 through 20...F108 - 126
691(chain F and (resid 16 or resid 19 through 20...F134
6101(chain F and (resid 16 or resid 19 through 20...F138
6111(chain F and (resid 16 or resid 19 through 20...F140
6121(chain F and (resid 16 or resid 19 through 20...F142
6131(chain F and (resid 16 or resid 19 through 20...F147 - 1159
6141(chain F and (resid 16 or resid 19 through 20...F161 - 179
6151(chain F and (resid 16 or resid 19 through 20...F18 - 179
6161(chain F and (resid 16 or resid 19 through 20...F181 - 245
6171(chain F and (resid 16 or resid 19 through 20...F247 - 259
6181(chain F and (resid 16 or resid 19 through 20...F261 - 333
6191(chain F and (resid 16 or resid 19 through 20...F335 - 341
6201(chain F and (resid 16 or resid 19 through 20...F344
6211(chain F and (resid 16 or resid 19 through 20...F384 - 420
6221(chain F and (resid 16 or resid 19 through 20...F422 - 463
6231(chain F and (resid 16 or resid 19 through 20...F465 - 471
6241(chain F and (resid 16 or resid 19 through 20...F473 - 489
6251(chain F and (resid 16 or resid 19 through 20...F491 - 493
6261(chain F and (resid 16 or resid 19 through 20...F495 - 530
6271(chain F and (resid 16 or resid 19 through 20...F532 - 584
6281(chain F and (resid 16 or resid 19 through 20...F586 - 598
112(chain G and (resid 14 through 73 or resid 75...G14 - 73
122(chain G and (resid 14 through 73 or resid 75...G75 - 124
132(chain G and (resid 14 through 73 or resid 75...G127 - 129
142(chain G and (resid 14 through 73 or resid 75...G138
152(chain G and (resid 14 through 73 or resid 75...G13 - 702
162(chain G and (resid 14 through 73 or resid 75...G13 - 702
172(chain G and (resid 14 through 73 or resid 75...G150 - 231
182(chain G and (resid 14 through 73 or resid 75...G354
192(chain G and (resid 14 through 73 or resid 75...G354
1102(chain G and (resid 14 through 73 or resid 75...G0
1112(chain G and (resid 14 through 73 or resid 75...G483 - 554
1122(chain G and (resid 14 through 73 or resid 75...G556 - 601
212(chain H and (resid 14 through 73 or resid 75...H14 - 73
222(chain H and (resid 14 through 73 or resid 75...H75 - 124
232(chain H and (resid 14 through 73 or resid 75...H127 - 129
242(chain H and (resid 14 through 73 or resid 75...H138
252(chain H and (resid 14 through 73 or resid 75...H13 - 702
262(chain H and (resid 14 through 73 or resid 75...H13 - 702
272(chain H and (resid 14 through 73 or resid 75...H150 - 231
282(chain H and (resid 14 through 73 or resid 75...H354
292(chain H and (resid 14 through 73 or resid 75...H354
2102(chain H and (resid 14 through 73 or resid 75...H0
2112(chain H and (resid 14 through 73 or resid 75...H483 - 554
2122(chain H and (resid 14 through 73 or resid 75...H556 - 601

NCS ensembles :
ID
1
2

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Components

#1: Protein
ATM1-type heavy metal exporter / ATP-binding cassette transporter Atm1 / NaAtm1


Mass: 67803.664 Da / Num. of mol.: 8 / Mutation: A527C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199) (bacteria)
Strain: ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199
Gene: atm1, Saro_2631 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G506
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
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: 3.82 Å3/Da / Density % sol: 67.77 % / Description: Thin plates
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: NaCl, MgCl2, Tris, PEG2000MME, ATP

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.97946
SYNCHROTRONSSRL BL12-220.97949
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJun 25, 2016
DECTRIS PILATUS 6M2PIXELNov 18, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Liquid nitrogen-cooled double crystal, non fixed exit slit Si(111)SINGLE WAVELENGTHMx-ray1
2Liquid nitrogen-cooled double crystal, non fixed exit slit Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.979491
Reflection

Entry-ID: 6PAM

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
3.7-39.618462897.557.1141.790.9990.1670.0670.1817.31
4.5-39.724727799.320.6163.640.9980.2910.0660.29828.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
3.7-3.8327.33.050.7476460.4121.2063.283189.28
4.5-4.6621.43.2411.446670.7610.7123.32299.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
REFMACrefinement
PHASERphasing
AutoSolphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MRN

4mrn


Resolution: 3.7→39.606 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.98
RfactorNum. reflection% reflection
Rfree0.2858 4185 5.01 %
Rwork0.2382 --
obs0.2406 83474 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 456.95 Å2 / Biso mean: 178.1364 Å2 / Biso min: 31.35 Å2
Refinement stepCycle: final / Resolution: 3.7→39.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36615 0 224 0 36839
Biso mean--194.08 --
Num. residues----4706
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14398X-RAY DIFFRACTION8.88TORSIONAL
12B14398X-RAY DIFFRACTION8.88TORSIONAL
13C14398X-RAY DIFFRACTION8.88TORSIONAL
14D14398X-RAY DIFFRACTION8.88TORSIONAL
15E14398X-RAY DIFFRACTION8.88TORSIONAL
16F14398X-RAY DIFFRACTION8.88TORSIONAL
21G5244X-RAY DIFFRACTION8.88TORSIONAL
22H5244X-RAY DIFFRACTION8.88TORSIONAL
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 (%)
3.7-3.7420.38121180.37612240235883
3.742-3.7860.44991170.35232465258291
3.786-3.83220.35681110.33672592270394
3.8322-3.88060.41121570.33632508266596
3.8806-3.93160.39541590.34812657281697
3.9316-3.98550.38791380.33612630276897
3.9855-4.04230.36911620.30652625278798
4.0423-4.10260.34531380.27822674281299
4.1026-4.16670.32081420.27362690283299
4.1667-4.23490.3711310.26512678280999
4.2349-4.30780.31341380.26282718285699
4.3078-4.38610.33771840.25442564274899
4.3861-4.47030.2991440.24312699284399
4.4703-4.56140.31011610.23352606276798
4.5614-4.66050.3021300.20662705283599
4.6605-4.76870.22771110.19172768287999
4.7687-4.88780.32041410.19042640278199
4.8878-5.01970.25681650.18552592275798
5.0197-5.16710.23351550.20012713286899
5.1671-5.33350.28161400.21182631277198
5.3335-5.52360.27151410.23152689283099
5.5236-5.74410.2981330.23882695282899
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