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- PDB-6x91: Crystal structure of MBP-fused human APOBEC1 -

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Basic information

Entry
Database: PDB / ID: 6x91
TitleCrystal structure of MBP-fused human APOBEC1
ComponentsMaltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
KeywordsHYDROLASE / APOBEC / RNA editing / deamination / metalloenzyme
Function / homology
Function and homology information


mRNA(cytosine6666) deaminase / mRNA editing complex / apolipoprotein B mRNA editing enzyme complex / mRNA Editing: C to U Conversion / Formation of the Editosome / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cytidine to uridine editing / negative regulation of triglyceride metabolic process / cytidine deaminase activity ...mRNA(cytosine6666) deaminase / mRNA editing complex / apolipoprotein B mRNA editing enzyme complex / mRNA Editing: C to U Conversion / Formation of the Editosome / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cytidine to uridine editing / negative regulation of triglyceride metabolic process / cytidine deaminase activity / positive regulation of gene expression via chromosomal CpG island demethylation / lipoprotein biosynthetic process / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / mRNA modification / triglyceride metabolic process / lipoprotein transport / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / response to gamma radiation / cell chemotaxis / establishment of localization in cell / lipid metabolic process / mRNA processing / regulation of cell population proliferation / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / RNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
C->U-editing enzyme APOBEC-1 / APOBEC4-like -AID/APOBEC-deaminase / APOBEC-like C-terminal domain / : / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...C->U-editing enzyme APOBEC-1 / APOBEC4-like -AID/APOBEC-deaminase / APOBEC-like C-terminal domain / : / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / CACODYLATE ION / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein / C->U-editing enzyme APOBEC-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsWolfe, A.D. / Li, S.-X. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: NAR Cancer / Year: 2020
Title: The structure of APOBEC1 and insights into its RNA and DNA substrate selectivity.
Authors: Wolfe, A.D. / Li, S. / Goedderz, C. / Chen, X.S.
History
DepositionJun 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
B: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
C: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
D: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
E: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
F: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
G: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
H: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)542,99838
Polymers536,5868
Non-polymers6,41130
Water00
1
A: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
B: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5789
Polymers134,1472
Non-polymers1,4327
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
D: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,92110
Polymers134,1472
Non-polymers1,7748
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
F: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5789
Polymers134,1472
Non-polymers1,4327
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
H: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,92110
Polymers134,1472
Non-polymers1,7748
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.715, 179.209, 210.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 92 or resid 94...
21(chain E and (resid 2 through 92 or resid 94...
12(chain B and (resid 3 through 14 or resid 16...
22(chain C and (resid 3 through 14 or resid 16...
32(chain D and (resid 3 through 14 or resid 16...
42(chain F and (resid 3 through 14 or resid 16...
52(chain G and (resid 3 through 14 or resid 16...
62(chain H and (resid 3 through 14 or resid 16...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 92 or resid 94...A2 - 92
121(chain A and (resid 2 through 92 or resid 94...A94 - 127
131(chain A and (resid 2 through 92 or resid 94...A2 - 1236
141(chain A and (resid 2 through 92 or resid 94...A1034 - 1234
151(chain A and (resid 2 through 92 or resid 94...A1301 - 1303
211(chain E and (resid 2 through 92 or resid 94...E2 - 92
221(chain E and (resid 2 through 92 or resid 94...E94 - 127
231(chain E and (resid 2 through 92 or resid 94...E129 - 1032
241(chain E and (resid 2 through 92 or resid 94...E1034 - 1234
251(chain E and (resid 2 through 92 or resid 94...E1301 - 1303
112(chain B and (resid 3 through 14 or resid 16...B3 - 14
122(chain B and (resid 3 through 14 or resid 16...B16 - 25
132(chain B and (resid 3 through 14 or resid 16...B27 - 85
142(chain B and (resid 3 through 14 or resid 16...B87 - 112
152(chain B and (resid 3 through 14 or resid 16...B122 - 127
162(chain B and (resid 3 through 14 or resid 16...B129
172(chain B and (resid 3 through 14 or resid 16...B131 - 140
182(chain B and (resid 3 through 14 or resid 16...B142 - 144
192(chain B and (resid 3 through 14 or resid 16...B151 - 155
1102(chain B and (resid 3 through 14 or resid 16...B207
1112(chain B and (resid 3 through 14 or resid 16...B207
1122(chain B and (resid 3 through 14 or resid 16...B209 - 225
1132(chain B and (resid 3 through 14 or resid 16...B228 - 258
1142(chain B and (resid 3 through 14 or resid 16...B260 - 264
1152(chain B and (resid 3 through 14 or resid 16...B267 - 273
1162(chain B and (resid 3 through 14 or resid 16...B276 - 2844
1172(chain B and (resid 3 through 14 or resid 16...B346 - 354
1182(chain B and (resid 3 through 14 or resid 16...B356354
1192(chain B and (resid 3 through 14 or resid 16...B356 - 367
1202(chain B and (resid 3 through 14 or resid 16...B371 - 1015
1212(chain B and (resid 3 through 14 or resid 16...B1018 - 1025
1222(chain B and (resid 3 through 14 or resid 16...B1029
1232(chain B and (resid 3 through 14 or resid 16...B1031 - 16
1242(chain B and (resid 3 through 14 or resid 16...B1045 - 1048
1252(chain B and (resid 3 through 14 or resid 16...B2 - 1236
1262(chain B and (resid 3 through 14 or resid 16...B1050 - 1072
1272(chain B and (resid 3 through 14 or resid 16...B1074
1282(chain B and (resid 3 through 14 or resid 16...B1078
1292(chain B and (resid 3 through 14 or resid 16...B1081 - 1093
1302(chain B and (resid 3 through 14 or resid 16...B1095 - 1101144
1312(chain B and (resid 3 through 14 or resid 16...B1146 - 1153
1322(chain B and (resid 3 through 14 or resid 16...B46 - 1153
1332(chain B and (resid 3 through 14 or resid 16...B1155 - 1162
1342(chain B and (resid 3 through 14 or resid 16...B1164 - 1206
1352(chain B and (resid 3 through 14 or resid 16...B1208 - 1231
1362(chain B and (resid 3 through 14 or resid 16...B1234
1372(chain B and (resid 3 through 14 or resid 16...B1303 - 1304
212(chain C and (resid 3 through 14 or resid 16...C3 - 14
222(chain C and (resid 3 through 14 or resid 16...C16 - 25
232(chain C and (resid 3 through 14 or resid 16...C27 - 85
242(chain C and (resid 3 through 14 or resid 16...C2 - 1236
252(chain C and (resid 3 through 14 or resid 16...C129
262(chain C and (resid 3 through 14 or resid 16...C2 - 1236
272(chain C and (resid 3 through 14 or resid 16...C2 - 1236
282(chain C and (resid 3 through 14 or resid 16...C4
292(chain C and (resid 3 through 14 or resid 16...C151 - 155
2102(chain C and (resid 3 through 14 or resid 16...C20
2112(chain C and (resid 3 through 14 or resid 16...C209 - 225
2122(chain C and (resid 3 through 14 or resid 16...C228 - 258
2132(chain C and (resid 3 through 14 or resid 16...C0
2142(chain C and (resid 3 through 14 or resid 16...C29
2152(chain C and (resid 3 through 14 or resid 16...C4
2162(chain C and (resid 3 through 14 or resid 16...C371 - 1015
2172(chain C and (resid 3 through 14 or resid 16...C1018 - 102
2182(chain C and (resid 3 through 14 or resid 16...C102029
2192(chain C and (resid 3 through 14 or resid 16...C1031 - 1032
2202(chain C and (resid 3 through 14 or resid 16...C10
2212(chain C and (resid 3 through 14 or resid 16...C1045 - 1048
2222(chain C and (resid 3 through 14 or resid 16...C1050 - 10
2232(chain C and (resid 3 through 14 or resid 16...C10
2242(chain C and (resid 3 through 14 or resid 16...C1095
2252(chain C and (resid 3 through 14 or resid 16...C1107 - 1144
2262(chain C and (resid 3 through 14 or resid 16...C0
2272(chain C and (resid 3 through 14 or resid 16...C1164 - 1206
2282(chain C and (resid 3 through 14 or resid 16...C1208 - 1231
2292(chain C and (resid 3 through 14 or resid 16...C1234
2302(chain C and (resid 3 through 14 or resid 16...C1303 - 1304
312(chain D and (resid 3 through 14 or resid 16...D3 - 14
322(chain D and (resid 3 through 14 or resid 16...D16 - 25
332(chain D and (resid 3 through 14 or resid 16...D27 - 85
342(chain D and (resid 3 through 14 or resid 16...D2 - 1236
352(chain D and (resid 3 through 14 or resid 16...D129
362(chain D and (resid 3 through 14 or resid 16...D2 - 1236
372(chain D and (resid 3 through 14 or resid 16...D2 - 1236
382(chain D and (resid 3 through 14 or resid 16...D5
392(chain D and (resid 3 through 14 or resid 16...D157 - 163
3102(chain D and (resid 3 through 14 or resid 16...D26
3112(chain D and (resid 3 through 14 or resid 16...D276 - 288
3122(chain D and (resid 3 through 14 or resid 16...D290 - 344
3132(chain D and (resid 3 through 14 or resid 16...D371
3142(chain D and (resid 3 through 14 or resid 16...D2 - 1236
3152(chain D and (resid 3 through 14 or resid 16...D1029
3162(chain D and (resid 3 through 14 or resid 16...D2 - 1236
3172(chain D and (resid 3 through 14 or resid 16...D1036
3182(chain D and (resid 3 through 14 or resid 16...D2 - 1236
3192(chain D and (resid 3 through 14 or resid 16...D1050 - 10
3202(chain D and (resid 3 through 14 or resid 16...D2 - 1236
3212(chain D and (resid 3 through 14 or resid 16...D1081 - 1093
3222(chain D and (resid 3 through 14 or resid 16...D1081 - 1093
3232(chain D and (resid 3 through 14 or resid 16...D1095
3242(chain D and (resid 3 through 14 or resid 16...D1146 - 1153
3252(chain D and (resid 3 through 14 or resid 16...D1155 - 1162
3262(chain D and (resid 3 through 14 or resid 16...D1164 - 1206
3272(chain D and (resid 3 through 14 or resid 16...D1208 - 1231
3282(chain D and (resid 3 through 14 or resid 16...D1208 - 1231
3292(chain D and (resid 3 through 14 or resid 16...D1234
3302(chain D and (resid 3 through 14 or resid 16...D1303 - 1304
412(chain F and (resid 3 through 14 or resid 16...F3 - 14
422(chain F and (resid 3 through 14 or resid 16...F16 - 25
432(chain F and (resid 3 through 14 or resid 16...F27 - 85
442(chain F and (resid 3 through 14 or resid 16...F122 - 127
452(chain F and (resid 3 through 14 or resid 16...F129
462(chain F and (resid 3 through 14 or resid 16...F131 - 140
472(chain F and (resid 3 through 14 or resid 16...F142 - 144
482(chain F and (resid 3 through 14 or resid 16...F151 - 155
492(chain F and (resid 3 through 14 or resid 16...F157 - 163
4102(chain F and (resid 3 through 14 or resid 16...F178 - 199
4112(chain F and (resid 3 through 14 or resid 16...F207
4122(chain F and (resid 3 through 14 or resid 16...F209 - 225
4132(chain F and (resid 3 through 14 or resid 16...F228 - 258
4142(chain F and (resid 3 through 14 or resid 16...F260 - 264
4152(chain F and (resid 3 through 14 or resid 16...F267 - 273
4162(chain F and (resid 3 through 14 or resid 16...F276 - 288
4172(chain F and (resid 3 through 14 or resid 16...F290 - 344
4182(chain F and (resid 3 through 14 or resid 16...F346 - 354
4192(chain F and (resid 3 through 14 or resid 16...F356 - 367
4202(chain F and (resid 3 through 14 or resid 16...F371 - 1015
4212(chain F and (resid 3 through 14 or resid 16...F1018 - 1025
4222(chain F and (resid 3 through 14 or resid 16...F1029
4232(chain F and (resid 3 through 14 or resid 16...F1031 - 1032
4242(chain F and (resid 3 through 14 or resid 16...F1036 - 1042
4252(chain F and (resid 3 through 14 or resid 16...F1045 - 1048
4262(chain F and (resid 3 through 14 or resid 16...F1050 - 1072
4272(chain F and (resid 3 through 14 or resid 16...F1074
4282(chain F and (resid 3 through 14 or resid 16...F1078
4292(chain F and (resid 3 through 14 or resid 16...F1081 - 1093
4302(chain F and (resid 3 through 14 or resid 16...F1095 - 1105
4312(chain F and (resid 3 through 14 or resid 16...F1107 - 1144
4322(chain F and (resid 3 through 14 or resid 16...F1146 - 1153
4332(chain F and (resid 3 through 14 or resid 16...F1155 - 1162
4342(chain F and (resid 3 through 14 or resid 16...F1164 - 1206
4352(chain F and (resid 3 through 14 or resid 16...F1208 - 1231
4362(chain F and (resid 3 through 14 or resid 16...F1234
4372(chain F and (resid 3 through 14 or resid 16...F1303 - 1304
512(chain G and (resid 3 through 14 or resid 16...G3 - 14
522(chain G and (resid 3 through 14 or resid 16...G16 - 25
532(chain G and (resid 3 through 14 or resid 16...G27 - 85
542(chain G and (resid 3 through 14 or resid 16...G122 - 127
552(chain G and (resid 3 through 14 or resid 16...G129
562(chain G and (resid 3 through 14 or resid 16...G131 - 140
572(chain G and (resid 3 through 14 or resid 16...G142 - 144
582(chain G and (resid 3 through 14 or resid 16...G151 - 155
592(chain G and (resid 3 through 14 or resid 16...G157 - 163
5102(chain G and (resid 3 through 14 or resid 16...G178 - 199
5112(chain G and (resid 3 through 14 or resid 16...G207
5122(chain G and (resid 3 through 14 or resid 16...G209 - 225
5132(chain G and (resid 3 through 14 or resid 16...G228 - 258
5142(chain G and (resid 3 through 14 or resid 16...G260 - 264
5152(chain G and (resid 3 through 14 or resid 16...G267 - 273
5162(chain G and (resid 3 through 14 or resid 16...G276 - 288
5172(chain G and (resid 3 through 14 or resid 16...G290 - 344
5182(chain G and (resid 3 through 14 or resid 16...G346 - 354
5192(chain G and (resid 3 through 14 or resid 16...G356 - 367
5202(chain G and (resid 3 through 14 or resid 16...G371 - 1015
5212(chain G and (resid 3 through 14 or resid 16...G1018 - 1025
5222(chain G and (resid 3 through 14 or resid 16...G1029
5232(chain G and (resid 3 through 14 or resid 16...G1031 - 1032
5242(chain G and (resid 3 through 14 or resid 16...G1036 - 1042
5252(chain G and (resid 3 through 14 or resid 16...G1045 - 1048
5262(chain G and (resid 3 through 14 or resid 16...G1050 - 1072
5272(chain G and (resid 3 through 14 or resid 16...G1074
5282(chain G and (resid 3 through 14 or resid 16...G1078
5292(chain G and (resid 3 through 14 or resid 16...G1081 - 1093
5302(chain G and (resid 3 through 14 or resid 16...G1095 - 1105
5312(chain G and (resid 3 through 14 or resid 16...G1107 - 1144
5322(chain G and (resid 3 through 14 or resid 16...G1146 - 1153
5332(chain G and (resid 3 through 14 or resid 16...G1155 - 1162
5342(chain G and (resid 3 through 14 or resid 16...G1164 - 1206
5352(chain G and (resid 3 through 14 or resid 16...G1208 - 1231
5362(chain G and (resid 3 through 14 or resid 16...G1234
5372(chain G and (resid 3 through 14 or resid 16...G1303 - 1304
612(chain H and (resid 3 through 14 or resid 16...H3 - 14
622(chain H and (resid 3 through 14 or resid 16...H16 - 25
632(chain H and (resid 3 through 14 or resid 16...H2 - 1236
642(chain H and (resid 3 through 14 or resid 16...H87 - 127
652(chain H and (resid 3 through 14 or resid 16...H129
662(chain H and (resid 3 through 14 or resid 16...H131 - 140
672(chain H and (resid 3 through 14 or resid 16...H142 - 155
682(chain H and (resid 3 through 14 or resid 16...H157 - 207
692(chain H and (resid 3 through 14 or resid 16...H209 - 258
6102(chain H and (resid 3 through 14 or resid 16...H29 - 258
6112(chain H and (resid 3 through 14 or resid 16...H260 - 273
6122(chain H and (resid 3 through 14 or resid 16...H276 - 288
6132(chain H and (resid 3 through 14 or resid 16...H290 - 344
6142(chain H and (resid 3 through 14 or resid 16...H346 - 354
6152(chain H and (resid 3 through 14 or resid 16...H356 - 36015
6162(chain H and (resid 3 through 14 or resid 16...H1018 - 1025
6172(chain H and (resid 3 through 14 or resid 16...H8 - 1025
6182(chain H and (resid 3 through 14 or resid 16...H1029
6192(chain H and (resid 3 through 14 or resid 16...H1031 - 1032
6202(chain H and (resid 3 through 14 or resid 16...H1036 - 1042
6212(chain H and (resid 3 through 14 or resid 16...H1045 - 1048
6222(chain H and (resid 3 through 14 or resid 16...H1051074
6232(chain H and (resid 3 through 14 or resid 16...H1078
6242(chain H and (resid 3 through 14 or resid 16...H108178
6252(chain H and (resid 3 through 14 or resid 16...H1081 - 1093
6262(chain H and (resid 3 through 14 or resid 16...H1095 - 1105
6272(chain H and (resid 3 through 14 or resid 16...H1107 - 1144
6282(chain H and (resid 3 through 14 or resid 16...H1146 - 1153
6292(chain H and (resid 3 through 14 or resid 16...H2 - 1236
6302(chain H and (resid 3 through 14 or resid 16...H1208 - 123
6312(chain H and (resid 3 through 14 or resid 16...H1234
6322(chain H and (resid 3 through 14 or resid 16...H1303 - 1304

NCS ensembles :
ID
1
2

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Components

#1: Protein
Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera / Apolipoprotein B mRNA-editing enzyme 1 / HEPR / mRNA(cytosine(6666)) deaminase 1


Mass: 67073.312 Da / Num. of mol.: 8
Mutation: A338V,M46A,R48S,E63A,M80T,W121M,A146D,L173A,W199A,F205A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: DAH37_23060, APOBEC1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4Z0THX4, UniProt: P41238, UniProt: P0AEX9*PLUS, mRNA(cytosine6666) deaminase
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6AsO2
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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M potassium chloride, 0.2 M magnesium acetate tetrahydrate, 0.05 M sodium cacodylate, pH 6.0, 8.5% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.28345 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28345 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 83654 / % possible obs: 99.2 % / Redundancy: 4.9 % / CC1/2: 0.883 / Net I/σ(I): 5.22
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.15 / Num. unique obs: 4100 / CC1/2: 0.213 / CC star: 0.593 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1ANF & 2NYT

1anf

2nyt


Resolution: 3.51→49.61 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 8334 9.99 %
Rwork0.2762 75124 -
obs0.2784 83458 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 295.45 Å2 / Biso mean: 136.6014 Å2 / Biso min: 40.72 Å2
Refinement stepCycle: final / Resolution: 3.51→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37254 0 370 0 37624
Biso mean--142.5 --
Num. residues----4667
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3540X-RAY DIFFRACTION7.049TORSIONAL
12E3540X-RAY DIFFRACTION7.049TORSIONAL
21B8514X-RAY DIFFRACTION7.049TORSIONAL
22C8514X-RAY DIFFRACTION7.049TORSIONAL
23D8514X-RAY DIFFRACTION7.049TORSIONAL
24F8514X-RAY DIFFRACTION7.049TORSIONAL
25G8514X-RAY DIFFRACTION7.049TORSIONAL
26H8514X-RAY DIFFRACTION7.049TORSIONAL
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 (%)
3.51-3.550.42432170.45652060227782
3.55-3.590.46582710.44312470274198
3.59-3.630.47512740.45532480275498
3.63-3.680.58212670.60792415268297
3.68-3.730.53982780.46592450272897
3.73-3.780.38852820.39522499278199
3.78-3.830.42522670.39262464273199
3.83-3.890.5012750.50712436271197
3.89-3.950.5462680.54142412268095
3.95-4.010.3922650.34022489275499
4.01-4.080.30882720.31652485275799
4.08-4.160.33772800.31022514279499
4.16-4.240.30732800.29732507278799
4.24-4.320.3182800.28512514279499
4.32-4.420.31322800.274225032783100
4.42-4.520.29042810.258825292810100
4.52-4.630.27682800.24324932773100
4.63-4.760.27122840.230725612845100
4.76-4.90.23512810.220824982779100
4.9-5.060.24032820.22225432825100
5.06-5.240.25462820.217925342816100
5.24-5.450.25312820.236325452827100
5.45-5.690.26242900.231625302820100
5.69-5.990.26562790.247325592838100
5.99-6.370.23332810.225625732854100
6.37-6.860.24752850.22625552840100
6.86-7.550.24182830.224325782861100
7.55-8.630.21512880.194925932881100
8.64-10.860.22870.166926092896100
10.86-49.610.263130.22982726303999
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)
11.7032-0.9827-0.77712.03851.31131.7507-0.06-0.3809-0.06630.03260.0877-0.30930.19490.3572-0.13070.73530.190.00211.2571-0.17661.2035-25.4868-30.9651-98.7993
20.95590.44350.57030.9078-0.28081.0972-0.29350.7542-1.0956-0.4736-0.3394-1.0567-0.05430.224-0.71620.2984-0.0485-0.01861.4987-0.53852.1815-8.956-9.8273-77.938
31.2177-1.61410.86582.6623-0.66463.7881-0.118-0.0079-0.57520.52320.1304-1.2184-0.30740.08620.1420.5362-0.0493-0.03811.1277-0.28951.396-21.40167.8405-68.4305
44.451.48271.35145.31121.13064.24010.06850.14930.318-0.5573-0.1311-0.85890.5290.29730.25430.7211-0.0168-0.21060.61850.09211.0744-13.168439.6979-61.3182
52.18930.96070.73154.4416-0.23812.4286-0.54530.35242.0752-0.2622-0.26080.4772-1.12930.07180.42361.0843-0.1168-0.43220.73780.44641.8632-15.667560.2112-67.7135
64.4310.1021.13123.47311.96453.32510.09990.63871.7501-1.21390.33731.3673-1.0989-0.30620.64590.8276-0.2055-0.36411.44860.31271.1247-33.25337.2887-82.3006
74.06231.97080.58034.17191.13984.41720.14290.21650.8399-0.9530.00122.0914-1.0015-0.17020.90990.8339-0.0047-0.41211.38010.00221.1633-44.881430.796-82.3249
81.84181.04471.28286.9998-0.15741.1095-0.31131.64750.1549-1.5975-0.6085-1.7623-0.01570.4098-0.26870.72720.39820.14631.64050.53671.0165-25.783127.8515-88.1657
95.1450.8051.93252.30480.66091.6997-0.34760.3123-0.6888-0.5892-0.45580.90330.30250.0816-0.50440.1454-0.186-0.4281.2003-0.57860.8662-35.86849.9879-77.0667
104.93830.60410.22852.99180.59192.19270.27420.0489-0.3636-0.17740.0639-0.0352-0.24620.4725-0.10950.3916-0.0924-0.13030.9657-0.3340.8951-91.7263-18.5852-85.5769
114.42330.4799-0.01012.6768-1.16122.00640.4723-0.6468-0.55720.269-0.22920.83130.3092-0.1255-0.14490.6896-0.1745-0.16030.79310.00080.78-91.0863-33.4991-70.427
123.99271.8128-0.67171.72710.55312.86790.3467-0.1718-0.24690.4857-0.13390.19950.1020.3201-0.05460.48360.0613-0.10341.0347-0.11591.2296-64.6039-15.7004-75.6477
134.48010.4398-0.11232.9852-1.04512.92630.02290.15780.01630.0396-0.1627-0.371-0.14510.56910.00750.35720.08490.07341.1028-0.26650.7246-58.5219-3.3275-84.2076
142.9826-0.856-0.46121.8471-0.63631.7437-0.7086-0.06090.54530.11461.4456-0.7833-1.20631.9497-0.01621.471-0.42630.51712.2938-0.0272.5609-32.600616.807-112.3217
154.58910.6637-0.54181.1615-1.5091.99050.45220.89132.1001-0.4362-0.405-0.60030.32391.4786-0.07541.5496-0.15290.52722.7940.24572.0488-24.16218.6221-130.7338
162.1262-0.8283-1.49972.84291.42571.2195-0.04820.80110.7543-2.0112-0.44630.0373-0.3693-0.2776-0.08871.348-0.11910.37542.46550.13831.1105-48.50881.0833-131.1866
173.51240.725-0.14513.00690.42754.19970.46681.00550.5673-0.9983-0.1319-0.31970.1117-0.2101-0.03460.8160.1035-0.20561.3669-0.06910.4172-64.32970.1205-117.0751
182.28-0.86811.09091.4023-0.581.77220.219-0.0145-0.3348-0.4975-0.12660.14180.45140.1633-0.14171.40920.2005-0.25190.72620.02841.190330.9225.8375-6.4951
191.5279-0.1328-0.3311.86230.43981.96180.16840.3514-1.01520.96050.1427-0.85790.2536-0.3320.41341.5147-0.1917-0.62320.0622-0.10632.23364.28613.081-30.443
205.04691.5403-0.08483.45260.37323.4219-0.2682-0.30670.10290.6712-0.19021.26820.0761-0.7620.37310.7091-0.030.19830.8506-0.23121.4857-55.414415.3135-39.1004
213.01210.7751.91163.83611.69661.89530.9805-1.38511.12710.0857-0.48961.4225-0.4845-0.3660.68561.4681-0.32380.22010.8428-0.37020.3897-37.144533.5998-23.1692
225.2331.17410.42844.76730.64872.4636-0.3979-0.87530.51850.4062-0.08910.51750.2396-0.5450.33751.23860.0001-0.08660.9224-0.37120.8978-29.536638.2757-21.0458
234.22961.21050.92594.54712.10351.4725-0.1721-0.04990.91320.0142-0.2214-0.3915-0.3609-0.0435-0.12071.2803-0.0643-0.38120.3099-0.33220.4773-9.81736.104-28.3763
243.4388-0.0201-0.87783.82610.53451.6279-0.08770.230.8397-0.06250.4049-0.359-0.0590.2755-0.15410.8964-0.1364-0.14210.5551-0.05170.549628.761393.491-29.9701
251.73390.9445-0.97413.53050.24061.5399-0.31390.0159-0.2709-0.61520.2606-0.54340.21780.419-0.12970.9078-0.19050.12780.8879-0.44771.328429.857778.8441-33.7292
262.28251.10620.67495.1302-1.27412.7626-0.51710.7925-0.0971-0.52430.22370.65820.52660.4042-0.16941.0870-0.3120.6626-0.10520.730913.657263.357-32.3817
273.00860.1410.05874.16150.15942.1235-0.212-0.0496-0.26440.29740.03360.16130.3816-0.0884-0.13641.09420.0756-0.25680.27760.03640.63273.065359.0279-20.6023
283.2566-0.47740.36641.732-0.24872.56030.61650.221-0.80270.5423-0.4781.61161.3988-0.5080.16462.1927-0.22660.15051.23260.49383.1903-19.309233.69478.828
291.16490.6785-1.08434.6470.01141.5089-0.4733-1.2466-0.350.92510.09791.8231.6361-0.1045-0.0942.9765-0.09720.19711.18240.67011.9344-14.114128.015125.2157
302.5820.3207-0.70833.38180.43631.91450.1548-1.5686-0.91271.3208-0.4834-0.41470.13040.13020.04262.10170.0994-0.02212.11960.06531.0938-3.003560.3428.5938
313.40890.93271.06423.53190.39654.086-0.0187-1.0169-0.40340.24660.31460.2235-0.26170.02130.0251.33730.1943-0.16770.8108-0.14750.51850.562264.94967.9872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 1038 )A2 - 1038
2X-RAY DIFFRACTION2chain 'A' and (resid 1039 through 1172 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1173 through 1236 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 83 )B2 - 83
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 369 )B84 - 369
6X-RAY DIFFRACTION6chain 'B' and (resid 370 through 1072 )B370 - 1072
7X-RAY DIFFRACTION7chain 'B' and (resid 1073 through 1136 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1137 through 1171 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1172 through 1236 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 97 )C2 - 97
11X-RAY DIFFRACTION11chain 'C' and (resid 98 through 366 )C98 - 366
12X-RAY DIFFRACTION12chain 'C' and (resid 367 through 1072 )C367 - 1072
13X-RAY DIFFRACTION13chain 'C' and (resid 1073 through 1236 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 83 )D2 - 83
15X-RAY DIFFRACTION15chain 'D' and (resid 84 through 352 )D84 - 352
16X-RAY DIFFRACTION16chain 'D' and (resid 353 through 1075 )D353 - 1075
17X-RAY DIFFRACTION17chain 'D' and (resid 1076 through 1236 )D0
18X-RAY DIFFRACTION18chain 'E' and (resid 2 through 1038 )E2 - 1038
19X-RAY DIFFRACTION19chain 'E' and (resid 1039 through 1236 )E0
20X-RAY DIFFRACTION20chain 'F' and (resid 2 through 369 )F2 - 369
21X-RAY DIFFRACTION21chain 'F' and (resid 370 through 1072 )F370 - 1072
22X-RAY DIFFRACTION22chain 'F' and (resid 1073 through 1171 )F0
23X-RAY DIFFRACTION23chain 'F' and (resid 1172 through 1236 )F0
24X-RAY DIFFRACTION24chain 'G' and (resid 2 through 315 )G2 - 315
25X-RAY DIFFRACTION25chain 'G' and (resid 316 through 1026 )G316 - 1026
26X-RAY DIFFRACTION26chain 'G' and (resid 1027 through 1075 )G0
27X-RAY DIFFRACTION27chain 'G' and (resid 1076 through 1236 )G0
28X-RAY DIFFRACTION28chain 'H' and (resid 2 through 97 )H2 - 97
29X-RAY DIFFRACTION29chain 'H' and (resid 98 through 1044 )H98 - 1044
30X-RAY DIFFRACTION30chain 'H' and (resid 1045 through 1106 )H0
31X-RAY DIFFRACTION31chain 'H' and (resid 1107 through 1236 )H0

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