[English] 日本語
Yorodumi
- PDB-6x91: Crystal structure of MBP-fused human APOBEC1 -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of triglyceride metabolic process / mRNA editing complex / apolipoprotein B mRNA editing enzyme complex / mRNA Editing: C to U Conversion / Formation of the Editosome / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / establishment of localization in cell / cytidine to uridine editing ...mRNA(cytosine6666) deaminase / negative regulation of triglyceride metabolic process / mRNA editing complex / apolipoprotein B mRNA editing enzyme complex / mRNA Editing: C to U Conversion / Formation of the Editosome / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / establishment of localization in cell / cytidine to uridine editing / lipoprotein transport / cytidine deaminase activity / lipoprotein biosynthetic process / positive regulation of gene expression via chromosomal CpG island demethylation / triglyceride metabolic process / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / mRNA modification / detection of maltose stimulus / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to gamma radiation / ATP-binding cassette (ABC) transporter complex / lipid metabolic process / cell chemotaxis / mRNA processing / regulation of cell population proliferation / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / RNA binding / nucleoplasm / zinc ion binding / membrane / nucleus / cytoplasm
Similarity search - Function
C->U-editing enzyme APOBEC-1 / APOBEC4-like -AID/APOBEC-deaminase / : / : / 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/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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 (eV)
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

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

New format data for meta-information of EMDB entries

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

Related info.:EMDB header

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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

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

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

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

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

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

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

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

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

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

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

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

+
Jul 12, 2017. Major update of PDB

Major update of PDB

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

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

-
Yorodumi

Thousand views of thousand structures

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

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

Read more