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- PDB-3ghq: Crystal Structure of E. coli W35F BFR mutant -

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Basic information

Entry
Database: PDB / ID: 3ghq
TitleCrystal Structure of E. coli W35F BFR mutant
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / BFR / W35F / Heme / Iron / Iron storage
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / membrane ...ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / membrane / identical protein binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Bacterioferritin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCrow, A. / Lawson, T.L. / Lewin, A. / Moore, G.R. / Le Brun, N.E.
CitationJournal: Biochemistry / Year: 2009
Title: Monitoring the iron status of the ferroxidase center of Escherichia coli bacterioferritin using fluorescence spectroscopy.
Authors: Lawson, T.L. / Crow, A. / Lewin, A. / Yasmin, S. / Moore, G.R. / Le Brun, N.E.
History
DepositionMar 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)228,13451
Polymers221,74812
Non-polymers6,38639
Water9,656536
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)456,268102
Polymers443,49524
Non-polymers12,77378
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area74370 Å2
ΔGint-256 kcal/mol
Surface area137020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.641, 207.641, 142.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
12B
22A
32C
42D
52E
62F
72G
82H
92I
102J
112K
122L
13C
23A
33B
43D
53E
63F
73G
83H
93I
103J
113K
123L
14D
24A
34B
44C
54E
64F
74G
84H
94I
104J
114K
124L
15E
25A
35B
45C
55D
65F
75G
85H
95I
105J
115K
125L
16F
26A
36B
46C
56D
66E
76G
86H
96I
106J
116K
126L
17G
27A
37B
47C
57D
67E
77F
87H
97I
107J
117K
127L
18H
28A
38B
48C
58D
68E
78F
88G
98I
108J
118K
128L
19I
29A
39B
49C
59D
69E
79F
89G
99H
109J
119K
129L
110J
210A
310B
410C
510D
610E
710F
810G
910H
1010I
1110K
1210L
111K
211A
311B
411C
511D
611E
711F
811G
911H
1011I
1111J
1211L
112L
212A
312B
412C
512D
612E
712F
812G
912H
1012I
1112J
1212K
113B
213D
313F
413H
513J
613L
114D
214B
314F
414H
514J
614L
115F
215B
315D
415H
515J
615L
116H
216B
316D
416F
516J
616L
117J
217B
317D
417F
517H
617L
118L
218B
318D
418F
518H
618J

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLYGLYAA1 - 1581 - 158
211METMETGLYGLYBB1 - 1581 - 158
311METMETGLYGLYCC1 - 1581 - 158
411METMETGLYGLYDD1 - 1581 - 158
511METMETGLYGLYEE1 - 1581 - 158
611METMETGLYGLYFF1 - 1581 - 158
711METMETGLYGLYGG1 - 1581 - 158
811METMETGLYGLYHH1 - 1581 - 158
911METMETGLYGLYII1 - 1581 - 158
1011METMETGLYGLYJJ1 - 1581 - 158
1111METMETGLYGLYKK1 - 1581 - 158
1211METMETGLYGLYLL1 - 1581 - 158
121FEFEFEFEAN300
221FEFEFEFEBS300
321FEFEFEFECV300
421FEFEFEFEDZ300
521FEFEFEFEEBA300
621FEFEFEFEFEA300
721FEFEFEFEGIA300
821FEFEFEFEHNA300
921FEFEFEFEIPA300
1021FEFEFEFEJSA300
1121FEFEFEFEKUA300
1221FEFEFEFELYA300
112METMETGLYGLYBB1 - 1581 - 158
212METMETGLYGLYAA1 - 1581 - 158
312METMETGLYGLYCC1 - 1581 - 158
412METMETGLYGLYDD1 - 1581 - 158
512METMETGLYGLYEE1 - 1581 - 158
612METMETGLYGLYFF1 - 1581 - 158
712METMETGLYGLYGG1 - 1581 - 158
812METMETGLYGLYHH1 - 1581 - 158
912METMETGLYGLYII1 - 1581 - 158
1012METMETGLYGLYJJ1 - 1581 - 158
1112METMETGLYGLYKK1 - 1581 - 158
1212METMETGLYGLYLL1 - 1581 - 158
122FEFEFEFEBS300
222FEFEFEFEAN300
322FEFEFEFECV300
422FEFEFEFEDZ300
522FEFEFEFEEBA300
622FEFEFEFEFEA300
722FEFEFEFEGIA300
822FEFEFEFEHNA300
922FEFEFEFEIPA300
1022FEFEFEFEJSA300
1122FEFEFEFEKUA300
1222FEFEFEFELYA300
113METMETGLYGLYCC1 - 1581 - 158
213METMETGLYGLYAA1 - 1581 - 158
313METMETGLYGLYBB1 - 1581 - 158
413METMETGLYGLYDD1 - 1581 - 158
513METMETGLYGLYEE1 - 1581 - 158
613METMETGLYGLYFF1 - 1581 - 158
713METMETGLYGLYGG1 - 1581 - 158
813METMETGLYGLYHH1 - 1581 - 158
913METMETGLYGLYII1 - 1581 - 158
1013METMETGLYGLYJJ1 - 1581 - 158
1113METMETGLYGLYKK1 - 1581 - 158
1213METMETGLYGLYLL1 - 1581 - 158
123FEFEFEFECV300
223FEFEFEFEAN300
323FEFEFEFEBS300
423FEFEFEFEDZ300
523FEFEFEFEEBA300
623FEFEFEFEFEA300
723FEFEFEFEGIA300
823FEFEFEFEHNA300
923FEFEFEFEIPA300
1023FEFEFEFEJSA300
1123FEFEFEFEKUA300
1223FEFEFEFELYA300
114METMETGLYGLYDD1 - 1581 - 158
214METMETGLYGLYAA1 - 1581 - 158
314METMETGLYGLYBB1 - 1581 - 158
414METMETGLYGLYCC1 - 1581 - 158
514METMETGLYGLYEE1 - 1581 - 158
614METMETGLYGLYFF1 - 1581 - 158
714METMETGLYGLYGG1 - 1581 - 158
814METMETGLYGLYHH1 - 1581 - 158
914METMETGLYGLYII1 - 1581 - 158
1014METMETGLYGLYJJ1 - 1581 - 158
1114METMETGLYGLYKK1 - 1581 - 158
1214METMETGLYGLYLL1 - 1581 - 158
124FEFEFEFEDZ300
224FEFEFEFEAN300
324FEFEFEFEBS300
424FEFEFEFECV300
524FEFEFEFEEBA300
624FEFEFEFEFEA300
724FEFEFEFEGIA300
824FEFEFEFEHNA300
924FEFEFEFEIPA300
1024FEFEFEFEJSA300
1124FEFEFEFEKUA300
1224FEFEFEFELYA300
115METMETGLYGLYEE1 - 1581 - 158
215METMETGLYGLYAA1 - 1581 - 158
315METMETGLYGLYBB1 - 1581 - 158
415METMETGLYGLYCC1 - 1581 - 158
515METMETGLYGLYDD1 - 1581 - 158
615METMETGLYGLYFF1 - 1581 - 158
715METMETGLYGLYGG1 - 1581 - 158
815METMETGLYGLYHH1 - 1581 - 158
915METMETGLYGLYII1 - 1581 - 158
1015METMETGLYGLYJJ1 - 1581 - 158
1115METMETGLYGLYKK1 - 1581 - 158
1215METMETGLYGLYLL1 - 1581 - 158
125FEFEFEFEEBA300
225FEFEFEFEAN300
325FEFEFEFEBS300
425FEFEFEFECV300
525FEFEFEFEDZ300
625FEFEFEFEFEA300
725FEFEFEFEGIA300
825FEFEFEFEHNA300
925FEFEFEFEIPA300
1025FEFEFEFEJSA300
1125FEFEFEFEKUA300
1225FEFEFEFELYA300
116METMETGLYGLYFF1 - 1581 - 158
216METMETGLYGLYAA1 - 1581 - 158
316METMETGLYGLYBB1 - 1581 - 158
416METMETGLYGLYCC1 - 1581 - 158
516METMETGLYGLYDD1 - 1581 - 158
616METMETGLYGLYEE1 - 1581 - 158
716METMETGLYGLYGG1 - 1581 - 158
816METMETGLYGLYHH1 - 1581 - 158
916METMETGLYGLYII1 - 1581 - 158
1016METMETGLYGLYJJ1 - 1581 - 158
1116METMETGLYGLYKK1 - 1581 - 158
1216METMETGLYGLYLL1 - 1581 - 158
126FEFEFEFEFEA300
226FEFEFEFEAN300
326FEFEFEFEBS300
426FEFEFEFECV300
526FEFEFEFEDZ300
626FEFEFEFEEBA300
726FEFEFEFEGIA300
826FEFEFEFEHNA300
926FEFEFEFEIPA300
1026FEFEFEFEJSA300
1126FEFEFEFEKUA300
1226FEFEFEFELYA300
117METMETGLYGLYGG1 - 1581 - 158
217METMETGLYGLYAA1 - 1581 - 158
317METMETGLYGLYBB1 - 1581 - 158
417METMETGLYGLYCC1 - 1581 - 158
517METMETGLYGLYDD1 - 1581 - 158
617METMETGLYGLYEE1 - 1581 - 158
717METMETGLYGLYFF1 - 1581 - 158
817METMETGLYGLYHH1 - 1581 - 158
917METMETGLYGLYII1 - 1581 - 158
1017METMETGLYGLYJJ1 - 1581 - 158
1117METMETGLYGLYKK1 - 1581 - 158
1217METMETGLYGLYLL1 - 1581 - 158
127FEFEFEFEGIA300
227FEFEFEFEAN300
327FEFEFEFEBS300
427FEFEFEFECV300
527FEFEFEFEDZ300
627FEFEFEFEEBA300
727FEFEFEFEFEA300
827FEFEFEFEHNA300
927FEFEFEFEIPA300
1027FEFEFEFEJSA300
1127FEFEFEFEKUA300
1227FEFEFEFELYA300
118METMETGLYGLYHH1 - 1581 - 158
218METMETGLYGLYAA1 - 1581 - 158
318METMETGLYGLYBB1 - 1581 - 158
418METMETGLYGLYCC1 - 1581 - 158
518METMETGLYGLYDD1 - 1581 - 158
618METMETGLYGLYEE1 - 1581 - 158
718METMETGLYGLYFF1 - 1581 - 158
818METMETGLYGLYGG1 - 1581 - 158
918METMETGLYGLYII1 - 1581 - 158
1018METMETGLYGLYJJ1 - 1581 - 158
1118METMETGLYGLYKK1 - 1581 - 158
1218METMETGLYGLYLL1 - 1581 - 158
128FEFEFEFEHNA300
228FEFEFEFEAN300
328FEFEFEFEBS300
428FEFEFEFECV300
528FEFEFEFEDZ300
628FEFEFEFEEBA300
728FEFEFEFEFEA300
828FEFEFEFEGIA300
928FEFEFEFEIPA300
1028FEFEFEFEJSA300
1128FEFEFEFEKUA300
1228FEFEFEFELYA300
119METMETGLYGLYII1 - 1581 - 158
219METMETGLYGLYAA1 - 1581 - 158
319METMETGLYGLYBB1 - 1581 - 158
419METMETGLYGLYCC1 - 1581 - 158
519METMETGLYGLYDD1 - 1581 - 158
619METMETGLYGLYEE1 - 1581 - 158
719METMETGLYGLYFF1 - 1581 - 158
819METMETGLYGLYGG1 - 1581 - 158
919METMETGLYGLYHH1 - 1581 - 158
1019METMETGLYGLYJJ1 - 1581 - 158
1119METMETGLYGLYKK1 - 1581 - 158
1219METMETGLYGLYLL1 - 1581 - 158
129FEFEFEFEIPA300
229FEFEFEFEAN300
329FEFEFEFEBS300
429FEFEFEFECV300
529FEFEFEFEDZ300
629FEFEFEFEEBA300
729FEFEFEFEFEA300
829FEFEFEFEGIA300
929FEFEFEFEHNA300
1029FEFEFEFEJSA300
1129FEFEFEFEKUA300
1229FEFEFEFELYA300
1110METMETGLYGLYJJ1 - 1581 - 158
2110METMETGLYGLYAA1 - 1581 - 158
3110METMETGLYGLYBB1 - 1581 - 158
4110METMETGLYGLYCC1 - 1581 - 158
5110METMETGLYGLYDD1 - 1581 - 158
6110METMETGLYGLYEE1 - 1581 - 158
7110METMETGLYGLYFF1 - 1581 - 158
8110METMETGLYGLYGG1 - 1581 - 158
9110METMETGLYGLYHH1 - 1581 - 158
10110METMETGLYGLYII1 - 1581 - 158
11110METMETGLYGLYKK1 - 1581 - 158
12110METMETGLYGLYLL1 - 1581 - 158
1210FEFEFEFEJSA300
2210FEFEFEFEAN300
3210FEFEFEFEBS300
4210FEFEFEFECV300
5210FEFEFEFEDZ300
6210FEFEFEFEEBA300
7210FEFEFEFEFEA300
8210FEFEFEFEGIA300
9210FEFEFEFEHNA300
10210FEFEFEFEIPA300
11210FEFEFEFEKUA300
12210FEFEFEFELYA300
1111METMETGLYGLYKK1 - 1581 - 158
2111METMETGLYGLYAA1 - 1581 - 158
3111METMETGLYGLYBB1 - 1581 - 158
4111METMETGLYGLYCC1 - 1581 - 158
5111METMETGLYGLYDD1 - 1581 - 158
6111METMETGLYGLYEE1 - 1581 - 158
7111METMETGLYGLYFF1 - 1581 - 158
8111METMETGLYGLYGG1 - 1581 - 158
9111METMETGLYGLYHH1 - 1581 - 158
10111METMETGLYGLYII1 - 1581 - 158
11111METMETGLYGLYJJ1 - 1581 - 158
12111METMETGLYGLYLL1 - 1581 - 158
1211FEFEFEFEKUA300
2211FEFEFEFEAN300
3211FEFEFEFEBS300
4211FEFEFEFECV300
5211FEFEFEFEDZ300
6211FEFEFEFEEBA300
7211FEFEFEFEFEA300
8211FEFEFEFEGIA300
9211FEFEFEFEHNA300
10211FEFEFEFEIPA300
11211FEFEFEFEJSA300
12211FEFEFEFELYA300
1112METMETGLYGLYLL1 - 1581 - 158
2112METMETGLYGLYAA1 - 1581 - 158
3112METMETGLYGLYBB1 - 1581 - 158
4112METMETGLYGLYCC1 - 1581 - 158
5112METMETGLYGLYDD1 - 1581 - 158
6112METMETGLYGLYEE1 - 1581 - 158
7112METMETGLYGLYFF1 - 1581 - 158
8112METMETGLYGLYGG1 - 1581 - 158
9112METMETGLYGLYHH1 - 1581 - 158
10112METMETGLYGLYII1 - 1581 - 158
11112METMETGLYGLYJJ1 - 1581 - 158
12112METMETGLYGLYKK1 - 1581 - 158
1212FEFEFEFELYA300
2212FEFEFEFEAN300
3212FEFEFEFEBS300
4212FEFEFEFECV300
5212FEFEFEFEDZ300
6212FEFEFEFEEBA300
7212FEFEFEFEFEA300
8212FEFEFEFEGIA300
9212FEFEFEFEHNA300
10212FEFEFEFEIPA300
11212FEFEFEFEJSA300
12212FEFEFEFEKUA300
1113HEMHEMHEMHEMAO200
2113HEMHEMHEMHEMDX200
3113HEMHEMHEMHEMFCA200
4113HEMHEMHEMHEMGJA200
5113HEMHEMHEMHEMIQA200
6113HEMHEMHEMHEMLWA200
1114HEMHEMHEMHEMDX200
2114HEMHEMHEMHEMAO200
3114HEMHEMHEMHEMFCA200
4114HEMHEMHEMHEMGJA200
5114HEMHEMHEMHEMIQA200
6114HEMHEMHEMHEMLWA200
1115HEMHEMHEMHEMFCA200
2115HEMHEMHEMHEMAO200
3115HEMHEMHEMHEMDX200
4115HEMHEMHEMHEMGJA200
5115HEMHEMHEMHEMIQA200
6115HEMHEMHEMHEMLWA200
1116HEMHEMHEMHEMGJA200
2116HEMHEMHEMHEMAO200
3116HEMHEMHEMHEMDX200
4116HEMHEMHEMHEMFCA200
5116HEMHEMHEMHEMIQA200
6116HEMHEMHEMHEMLWA200
1117HEMHEMHEMHEMIQA200
2117HEMHEMHEMHEMAO200
3117HEMHEMHEMHEMDX200
4117HEMHEMHEMHEMFCA200
5117HEMHEMHEMHEMGJA200
6117HEMHEMHEMHEMLWA200
1118HEMHEMHEMHEMLWA200
2118HEMHEMHEMHEMAO200
3118HEMHEMHEMHEMDX200
4118HEMHEMHEMHEMFCA200
5118HEMHEMHEMHEMGJA200
6118HEMHEMHEMHEMIQA200

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

#1: Protein
Bacterioferritin / / BFR / Cytochrome b-1 / Cytochrome b-557


Mass: 18478.979 Da / Num. of mol.: 12 / Mutation: W35F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b3336, bfr, JW3298 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABD3
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 289 K / pH: 5
Details: 2.45M Ammonium Sulfate, 0.1M sodium Citrate pH 5.0, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.7429 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7429 Å / Relative weight: 1
ReflectionResolution: 2.7→35 Å / Num. all: 81605 / Num. obs: 81605 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.4 % / Rsym value: 0.146 / Net I/σ(I): 17.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.469 / % possible all: 76.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E1J
Resolution: 2.7→34.61 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.647 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.866 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26169 4090 5 %RANDOM
Rwork0.24326 ---
obs0.24419 77457 95.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.481 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15876 0 375 536 16787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02116524
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5542.02622338
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.64551956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03824.805924
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.1153168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.96515132
X-RAY DIFFRACTIONr_chiral_restr0.1270.22328
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212612
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.28328
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.211199
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2649
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0140.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.2158
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.59828
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.206215240
X-RAY DIFFRACTIONr_scbond_it2.17237527
X-RAY DIFFRACTIONr_scangle_it3.4974.57074
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1324tight positional0.010.05
12B1324tight positional0.010.05
13C1324tight positional0.010.05
14D1324tight positional0.010.05
15E1324tight positional0.010.05
16F1324tight positional0.010.05
17G1324tight positional0.010.05
18H1324tight positional0.010.05
19I1324tight positional0.010.05
110J1324tight positional0.010.05
111K1324tight positional0.010.05
112L1324tight positional0.010.05
21B1324tight positional0.010.05
22A1324tight positional0.010.05
23C1324tight positional0.010.05
24D1324tight positional0.010.05
25E1324tight positional0.010.05
26F1324tight positional0.010.05
27G1324tight positional0.010.05
28H1324tight positional0.010.05
29I1324tight positional0.010.05
210J1324tight positional0.010.05
211K1324tight positional0.010.05
212L1324tight positional0.010.05
31C1324tight positional0.010.05
32A1324tight positional0.010.05
33B1324tight positional0.010.05
34D1324tight positional0.010.05
35E1324tight positional0.010.05
36F1324tight positional0.010.05
37G1324tight positional0.010.05
38H1324tight positional0.010.05
39I1324tight positional0.010.05
310J1324tight positional0.010.05
311K1324tight positional0.010.05
312L1324tight positional0.010.05
41D1324tight positional0.010.05
42A1324tight positional0.010.05
43B1324tight positional0.010.05
44C1324tight positional0.010.05
45E1324tight positional0.010.05
46F1324tight positional0.010.05
47G1324tight positional0.010.05
48H1324tight positional0.010.05
49I1324tight positional0.010.05
410J1324tight positional0.010.05
411K1324tight positional0.010.05
412L1324tight positional0.010.05
51E1324tight positional0.010.05
52A1324tight positional0.010.05
53B1324tight positional0.010.05
54C1324tight positional0.010.05
55D1324tight positional0.010.05
56F1324tight positional0.010.05
57G1324tight positional0.010.05
58H1324tight positional0.010.05
59I1324tight positional0.010.05
510J1324tight positional0.010.05
511K1324tight positional0.010.05
512L1324tight positional0.010.05
61F1324tight positional0.010.05
62A1324tight positional0.010.05
63B1324tight positional0.010.05
64C1324tight positional0.010.05
65D1324tight positional0.010.05
66E1324tight positional0.010.05
67G1324tight positional0.010.05
68H1324tight positional0.010.05
69I1324tight positional0.010.05
610J1324tight positional0.010.05
611K1324tight positional0.010.05
612L1324tight positional0.010.05
71G1324tight positional0.010.05
72A1324tight positional0.010.05
73B1324tight positional0.010.05
74C1324tight positional0.010.05
75D1324tight positional0.010.05
76E1324tight positional0.010.05
77F1324tight positional0.010.05
78H1324tight positional0.010.05
79I1324tight positional0.010.05
710J1324tight positional0.010.05
711K1324tight positional0.010.05
712L1324tight positional0.010.05
81H1324tight positional0.010.05
82A1324tight positional0.010.05
83B1324tight positional0.010.05
84C1324tight positional0.010.05
85D1324tight positional0.010.05
86E1324tight positional0.010.05
87F1324tight positional0.010.05
88G1324tight positional0.010.05
89I1324tight positional0.010.05
810J1324tight positional0.010.05
811K1324tight positional0.010.05
812L1324tight positional0.010.05
91I1324tight positional0.010.05
92A1324tight positional0.010.05
93B1324tight positional0.010.05
94C1324tight positional0.010.05
95D1324tight positional0.010.05
96E1324tight positional0.010.05
97F1324tight positional0.010.05
98G1324tight positional0.010.05
99H1324tight positional0.010.05
910J1324tight positional0.010.05
911K1324tight positional0.010.05
912L1324tight positional0.010.05
101J1324tight positional0.010.05
102A1324tight positional0.010.05
103B1324tight positional0.010.05
104C1324tight positional0.010.05
105D1324tight positional0.010.05
106E1324tight positional0.010.05
107F1324tight positional0.010.05
108G1324tight positional0.010.05
109H1324tight positional0.010.05
1010I1324tight positional0.010.05
1011K1324tight positional0.010.05
1012L1324tight positional0.010.05
111K1324tight positional0.010.05
112A1324tight positional0.010.05
113B1324tight positional0.010.05
114C1324tight positional0.010.05
115D1324tight positional0.010.05
116E1324tight positional0.010.05
117F1324tight positional0.010.05
118G1324tight positional0.010.05
119H1324tight positional0.010.05
1110I1324tight positional0.010.05
1111J1324tight positional0.010.05
1112L1324tight positional0.010.05
121L1324tight positional0.010.05
122A1324tight positional0.010.05
123B1324tight positional0.010.05
124C1324tight positional0.010.05
125D1324tight positional0.010.05
126E1324tight positional0.010.05
127F1324tight positional0.010.05
128G1324tight positional0.010.05
129H1324tight positional0.010.05
1210I1324tight positional0.010.05
1211J1324tight positional0.010.05
1212K1324tight positional0.010.05
131B43tight positional00.05
132D43tight positional00.05
133F43tight positional00.05
134H43tight positional00.05
135J43tight positional00.05
136L43tight positional0.010.05
141D43tight positional00.05
142B43tight positional00.05
143F43tight positional00.05
144H43tight positional00.05
145J43tight positional00.05
146L43tight positional0.010.05
151F43tight positional00.05
152B43tight positional00.05
153D43tight positional00.05
154H43tight positional00.05
155J43tight positional00.05
156L43tight positional0.010.05
161H43tight positional00.05
162B43tight positional00.05
163D43tight positional00.05
164F43tight positional00.05
165J43tight positional00.05
166L43tight positional0.010.05
171J43tight positional00.05
172B43tight positional00.05
173D43tight positional00.05
174F43tight positional00.05
175H43tight positional00.05
176L43tight positional0.010.05
181L43tight positional0.010.05
182B43tight positional00.05
183D43tight positional00.05
184F43tight positional00.05
185H43tight positional00.05
186J43tight positional00.05
11A1324tight thermal0.010.5
12B1324tight thermal0.010.5
13C1324tight thermal0.010.5
14D1324tight thermal0.010.5
15E1324tight thermal0.010.5
16F1324tight thermal0.010.5
17G1324tight thermal0.010.5
18H1324tight thermal0.010.5
19I1324tight thermal0.010.5
110J1324tight thermal0.010.5
111K1324tight thermal0.010.5
112L1324tight thermal0.010.5
21B1324tight thermal0.010.5
22A1324tight thermal0.010.5
23C1324tight thermal0.010.5
24D1324tight thermal0.010.5
25E1324tight thermal0.010.5
26F1324tight thermal0.010.5
27G1324tight thermal0.010.5
28H1324tight thermal0.010.5
29I1324tight thermal0.010.5
210J1324tight thermal0.010.5
211K1324tight thermal0.010.5
212L1324tight thermal0.010.5
31C1324tight thermal0.010.5
32A1324tight thermal0.010.5
33B1324tight thermal0.010.5
34D1324tight thermal0.010.5
35E1324tight thermal0.010.5
36F1324tight thermal0.010.5
37G1324tight thermal0.010.5
38H1324tight thermal0.010.5
39I1324tight thermal0.010.5
310J1324tight thermal0.010.5
311K1324tight thermal0.010.5
312L1324tight thermal0.010.5
41D1324tight thermal0.010.5
42A1324tight thermal0.010.5
43B1324tight thermal0.010.5
44C1324tight thermal0.010.5
45E1324tight thermal0.010.5
46F1324tight thermal0.010.5
47G1324tight thermal0.010.5
48H1324tight thermal0.010.5
49I1324tight thermal0.010.5
410J1324tight thermal0.010.5
411K1324tight thermal0.010.5
412L1324tight thermal0.010.5
51E1324tight thermal0.010.5
52A1324tight thermal0.010.5
53B1324tight thermal0.010.5
54C1324tight thermal0.010.5
55D1324tight thermal0.010.5
56F1324tight thermal0.010.5
57G1324tight thermal0.010.5
58H1324tight thermal0.010.5
59I1324tight thermal0.010.5
510J1324tight thermal0.010.5
511K1324tight thermal0.010.5
512L1324tight thermal0.010.5
61F1324tight thermal0.010.5
62A1324tight thermal0.010.5
63B1324tight thermal0.010.5
64C1324tight thermal0.010.5
65D1324tight thermal0.010.5
66E1324tight thermal0.010.5
67G1324tight thermal0.010.5
68H1324tight thermal0.010.5
69I1324tight thermal0.010.5
610J1324tight thermal0.010.5
611K1324tight thermal0.010.5
612L1324tight thermal0.010.5
71G1324tight thermal0.010.5
72A1324tight thermal0.010.5
73B1324tight thermal0.010.5
74C1324tight thermal0.010.5
75D1324tight thermal0.010.5
76E1324tight thermal0.010.5
77F1324tight thermal0.010.5
78H1324tight thermal0.010.5
79I1324tight thermal0.010.5
710J1324tight thermal0.010.5
711K1324tight thermal0.010.5
712L1324tight thermal0.010.5
81H1324tight thermal0.010.5
82A1324tight thermal0.010.5
83B1324tight thermal0.010.5
84C1324tight thermal0.010.5
85D1324tight thermal0.010.5
86E1324tight thermal0.010.5
87F1324tight thermal0.010.5
88G1324tight thermal0.010.5
89I1324tight thermal0.010.5
810J1324tight thermal0.010.5
811K1324tight thermal0.010.5
812L1324tight thermal0.010.5
91I1324tight thermal0.010.5
92A1324tight thermal0.010.5
93B1324tight thermal0.010.5
94C1324tight thermal0.010.5
95D1324tight thermal0.010.5
96E1324tight thermal0.010.5
97F1324tight thermal0.010.5
98G1324tight thermal0.010.5
99H1324tight thermal0.010.5
910J1324tight thermal0.010.5
911K1324tight thermal0.010.5
912L1324tight thermal0.010.5
101J1324tight thermal0.010.5
102A1324tight thermal0.010.5
103B1324tight thermal0.010.5
104C1324tight thermal0.010.5
105D1324tight thermal0.010.5
106E1324tight thermal0.010.5
107F1324tight thermal0.010.5
108G1324tight thermal0.010.5
109H1324tight thermal0.010.5
1010I1324tight thermal0.010.5
1011K1324tight thermal0.010.5
1012L1324tight thermal0.010.5
111K1324tight thermal0.010.5
112A1324tight thermal0.010.5
113B1324tight thermal0.010.5
114C1324tight thermal0.010.5
115D1324tight thermal0.010.5
116E1324tight thermal0.010.5
117F1324tight thermal0.010.5
118G1324tight thermal0.010.5
119H1324tight thermal0.010.5
1110I1324tight thermal0.010.5
1111J1324tight thermal0.010.5
1112L1324tight thermal0.010.5
121L1324tight thermal0.010.5
122A1324tight thermal0.010.5
123B1324tight thermal0.010.5
124C1324tight thermal0.010.5
125D1324tight thermal0.010.5
126E1324tight thermal0.010.5
127F1324tight thermal0.010.5
128G1324tight thermal0.010.5
129H1324tight thermal0.010.5
1210I1324tight thermal0.010.5
1211J1324tight thermal0.010.5
1212K1324tight thermal0.010.5
131B43tight thermal0.010.5
132D43tight thermal0.010.5
133F43tight thermal0.010.5
134H43tight thermal0.010.5
135J43tight thermal0.010.5
136L43tight thermal0.010.5
141D43tight thermal0.010.5
142B43tight thermal0.010.5
143F43tight thermal0.010.5
144H43tight thermal0.010.5
145J43tight thermal0.010.5
146L43tight thermal0.010.5
151F43tight thermal0.010.5
152B43tight thermal0.010.5
153D43tight thermal0.010.5
154H43tight thermal0.010.5
155J43tight thermal0.010.5
156L43tight thermal0.010.5
161H43tight thermal0.010.5
162B43tight thermal0.010.5
163D43tight thermal0.010.5
164F43tight thermal0.010.5
165J43tight thermal0.010.5
166L43tight thermal0.010.5
171J43tight thermal0.010.5
172B43tight thermal0.010.5
173D43tight thermal0.010.5
174F43tight thermal0.010.5
175H43tight thermal0.010.5
176L43tight thermal0.010.5
181L43tight thermal0.010.5
182B43tight thermal0.010.5
183D43tight thermal0.010.5
184F43tight thermal0.010.5
185H43tight thermal0.010.5
186J43tight thermal0.010.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 227 -
Rwork0.382 4260 -
obs--72.39 %

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