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- PDB-5yb0: Crystal Structure of Wild Type Phosphoserine aminotransferase (PS... -

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Basic information

Entry
Database: PDB / ID: 5yb0
TitleCrystal Structure of Wild Type Phosphoserine aminotransferase (PSAT) from E. histolytica
ComponentsPhosphoserine aminotransferase
KeywordsTRANSFERASE / PHOSPHOSERINE AMINOTRANSFERASE
Function / homology
Function and homology information


phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / L-serine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Phosphoserine aminotransferase / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Phosphoserine aminotransferase / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / phosphoserine transaminase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.94 Å
AuthorsSingh, R.K. / Gourinath, S.
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: N-terminal residues are crucial for quaternary structure and active site conformation for the phosphoserine aminotransferase from enteric human parasite E. histolytica.
Authors: Singh, R.K. / Tomar, P. / Dharavath, S. / Kumar, S. / Gourinath, S.
History
DepositionSep 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3May 8, 2024Group: Advisory / Derived calculations / Refinement description
Category: pdbx_validate_close_contact / software / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)489,66827
Polymers487,02012
Non-polymers2,64915
Water2,792155
1
A: Phosphoserine aminotransferase
B: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7356
Polymers81,1702
Non-polymers5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Phosphoserine aminotransferase
D: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7356
Polymers81,1702
Non-polymers5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Phosphoserine aminotransferase
H: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7005
Polymers81,1702
Non-polymers5303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Phosphoserine aminotransferase
G: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6644
Polymers81,1702
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Phosphoserine aminotransferase
J: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4173
Polymers81,1702
Non-polymers2471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Phosphoserine aminotransferase
L: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4173
Polymers81,1702
Non-polymers2471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.446, 134.073, 139.064
Angle α, β, γ (deg.)62.85, 88.58, 74.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112B
212C
113B
213D
114B
214E
115B
215F
116B
216G
117B
217H
118B
218I
119B
219J
120B
220K
121B
221L
122C
222D
123C
223E
124C
224F
125C
225G
126C
226H
127C
227I
128C
228J
129C
229K
130C
230L
131D
231E
132D
232F
133D
233G
134D
234H
135D
235I
136D
236J
137D
237K
138D
238L
139E
239F
140E
240G
141E
241H
142E
242I
143E
243J
144E
244K
145E
245L
146F
246G
147F
247H
148F
248I
149F
249J
150F
250K
151F
251L
152G
252H
153G
253I
154G
254J
155G
255K
156G
256L
157H
257I
158H
258J
159H
259K
160H
260L
161I
261J
162I
262K
163I
263L
164J
264K
165J
265L
166K
266L

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLUGLUAA7 - 3537 - 353
21HISHISGLUGLUBB7 - 3537 - 353
12HISHISGLUGLUAA7 - 3537 - 353
22HISHISGLUGLUCC7 - 3537 - 353
13HISHISGLNGLNAA7 - 3547 - 354
23HISHISGLNGLNDD7 - 3547 - 354
14HISHISGLUGLUAA7 - 3537 - 353
24HISHISGLUGLUEE7 - 3537 - 353
15HISHISCYSCYSAA7 - 3487 - 348
25HISHISCYSCYSFF7 - 3487 - 348
16HISHISGLNGLNAA7 - 3547 - 354
26HISHISGLNGLNGG7 - 3547 - 354
17HISHISGLUGLUAA7 - 3537 - 353
27HISHISGLUGLUHH7 - 3537 - 353
18HISHISGLNGLNAA7 - 3547 - 354
28HISHISGLNGLNII7 - 3547 - 354
19PHEPHEGLUGLUAA9 - 2609 - 260
29PHEPHEGLUGLUJJ9 - 2609 - 260
110LEULEUPHEPHEAA38 - 35238 - 352
210LEULEUPHEPHEKK38 - 35238 - 352
111LEULEUILEILEAA35 - 24935 - 249
211LEULEUILEILELL35 - 24935 - 249
112ILEILEGLNGLNBB6 - 3546 - 354
212ILEILEGLNGLNCC6 - 3546 - 354
113ILEILEGLNGLNBB6 - 3546 - 354
213ILEILEGLNGLNDD6 - 3546 - 354
114ILEILEGLUGLUBB6 - 3536 - 353
214ILEILEGLUGLUEE6 - 3536 - 353
115ILEILECYSCYSBB6 - 3486 - 348
215ILEILECYSCYSFF6 - 3486 - 348
116ILEILEGLNGLNBB6 - 3546 - 354
216ILEILEGLNGLNGG6 - 3546 - 354
117ILEILEGLNGLNBB6 - 3546 - 354
217ILEILEGLNGLNHH6 - 3546 - 354
118ILEILEGLNGLNBB6 - 3546 - 354
218ILEILEGLNGLNII6 - 3546 - 354
119PHEPHEGLUGLUBB9 - 2609 - 260
219PHEPHEGLUGLUJJ9 - 2609 - 260
120LEULEUPHEPHEBB38 - 35238 - 352
220LEULEUPHEPHEKK38 - 35238 - 352
121LEULEUILEILEBB35 - 24935 - 249
221LEULEUILEILELL35 - 24935 - 249
122ILEILEGLNGLNCC6 - 3546 - 354
222ILEILEGLNGLNDD6 - 3546 - 354
123ILEILEGLUGLUCC6 - 3536 - 353
223ILEILEGLUGLUEE6 - 3536 - 353
124ILEILECYSCYSCC6 - 3486 - 348
224ILEILECYSCYSFF6 - 3486 - 348
125ILEILEGLNGLNCC6 - 3546 - 354
225ILEILEGLNGLNGG6 - 3546 - 354
126ILEILEGLNGLNCC6 - 3546 - 354
226ILEILEGLNGLNHH6 - 3546 - 354
127ILEILEGLNGLNCC6 - 3546 - 354
227ILEILEGLNGLNII6 - 3546 - 354
128PHEPHEGLUGLUCC9 - 2609 - 260
228PHEPHEGLUGLUJJ9 - 2609 - 260
129LEULEUPHEPHECC38 - 35238 - 352
229LEULEUPHEPHEKK38 - 35238 - 352
130LEULEUILEILECC35 - 24935 - 249
230LEULEUILEILELL35 - 24935 - 249
131ILEILEGLUGLUDD6 - 3536 - 353
231ILEILEGLUGLUEE6 - 3536 - 353
132ILEILECYSCYSDD6 - 3486 - 348
232ILEILECYSCYSFF6 - 3486 - 348
133ILEILEGLNGLNDD6 - 3546 - 354
233ILEILEGLNGLNGG6 - 3546 - 354
134ILEILEGLNGLNDD6 - 3546 - 354
234ILEILEGLNGLNHH6 - 3546 - 354
135ILEILEGLNGLNDD6 - 3546 - 354
235ILEILEGLNGLNII6 - 3546 - 354
136PHEPHEGLUGLUDD9 - 2609 - 260
236PHEPHEGLUGLUJJ9 - 2609 - 260
137LEULEUPHEPHEDD38 - 35238 - 352
237LEULEUPHEPHEKK38 - 35238 - 352
138LEULEUILEILEDD35 - 24935 - 249
238LEULEUILEILELL35 - 24935 - 249
139ILEILECYSCYSEE6 - 3486 - 348
239ILEILECYSCYSFF6 - 3486 - 348
140ILEILEGLUGLUEE6 - 3536 - 353
240ILEILEGLUGLUGG6 - 3536 - 353
141ILEILEGLUGLUEE6 - 3536 - 353
241ILEILEGLUGLUHH6 - 3536 - 353
142ILEILEGLUGLUEE6 - 3536 - 353
242ILEILEGLUGLUII6 - 3536 - 353
143PHEPHEGLUGLUEE9 - 2609 - 260
243PHEPHEGLUGLUJJ9 - 2609 - 260
144LEULEUPHEPHEEE38 - 35238 - 352
244LEULEUPHEPHEKK38 - 35238 - 352
145LEULEUILEILEEE35 - 24935 - 249
245LEULEUILEILELL35 - 24935 - 249
146ILEILECYSCYSFF6 - 3486 - 348
246ILEILECYSCYSGG6 - 3486 - 348
147ILEILECYSCYSFF6 - 3486 - 348
247ILEILECYSCYSHH6 - 3486 - 348
148ILEILECYSCYSFF6 - 3486 - 348
248ILEILECYSCYSII6 - 3486 - 348
149PHEPHEGLUGLUFF9 - 2609 - 260
249PHEPHEGLUGLUJJ9 - 2609 - 260
150LEULEULYSLYSFF38 - 34738 - 347
250LEULEULYSLYSKK38 - 34738 - 347
151LEULEUILEILEFF35 - 24935 - 249
251LEULEUILEILELL35 - 24935 - 249
152ILEILEGLNGLNGG6 - 3546 - 354
252ILEILEGLNGLNHH6 - 3546 - 354
153ILEILEGLNGLNGG6 - 3546 - 354
253ILEILEGLNGLNII6 - 3546 - 354
154PHEPHEGLUGLUGG9 - 2609 - 260
254PHEPHEGLUGLUJJ9 - 2609 - 260
155LEULEUPHEPHEGG38 - 35238 - 352
255LEULEUPHEPHEKK38 - 35238 - 352
156LEULEUILEILEGG35 - 24935 - 249
256LEULEUILEILELL35 - 24935 - 249
157ILEILEGLNGLNHH6 - 3546 - 354
257ILEILEGLNGLNII6 - 3546 - 354
158PHEPHEGLUGLUHH9 - 2609 - 260
258PHEPHEGLUGLUJJ9 - 2609 - 260
159LEULEUPHEPHEHH38 - 35238 - 352
259LEULEUPHEPHEKK38 - 35238 - 352
160LEULEUILEILEHH35 - 24935 - 249
260LEULEUILEILELL35 - 24935 - 249
161PHEPHEGLUGLUII9 - 2609 - 260
261PHEPHEGLUGLUJJ9 - 2609 - 260
162LEULEUPHEPHEII38 - 35238 - 352
262LEULEUPHEPHEKK38 - 35238 - 352
163LEULEUILEILEII35 - 24935 - 249
263LEULEUILEILELL35 - 24935 - 249
164LEULEUGLUGLUJJ38 - 26038 - 260
264LEULEUGLUGLUKK38 - 26038 - 260
165LEULEUILEILEJJ35 - 24935 - 249
265LEULEUILEILELL35 - 24935 - 249
166LEULEUILEILEKK38 - 24938 - 249
266LEULEUILEILELL38 - 24938 - 249

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.991396, -0.028755, -0.127698), (-0.028831, -0.999584, 0.00125), (-0.12768, 0.002443, -0.991812)-4.42575, -29.810089, -61.692909
3given(1), (1), (1)
4given(-0.997227, -0.004659, -0.074274), (0.031301, 0.879202, -0.47542), (0.067517, -0.476426, -0.876618)-9.85708, -17.743139, -135.035782
5given(1), (1), (1)
6given(-0.997919, 0.062511, 0.015802), (-0.047176, -0.874942, 0.481924), (0.043952, 0.480175, 0.876071)1.67634, -10.79655, 73.258339
7given(1), (1), (1)
8given(0.104575, 0.674384, 0.730938), (0.62579, -0.615846, 0.478666), (0.77295, 0.407357, -0.486425)39.960041, -41.27449, -23.780121
9given(1), (1), (1)
10given(0.018616, -0.717311, -0.696504), (0.604821, 0.562789, -0.563436), (0.796144, -0.410772, 0.444322)-23.14794, -54.646198, -6.91186
11given(1), (1), (1)
12given(-0.081285, -0.661993, -0.74509), (-0.605443, -0.561035, 0.564516), (-0.791727, 0.496996, -0.355195)-25.99765, 25.165211, -52.33287
13given(1), (1), (1)
14given(0.00126, 0.61889, 0.785476), (-0.623019, 0.614891, -0.483484), (-0.782206, -0.488757, 0.386355)38.661049, 11.60818, -43.534389
15given(1), (1), (1)
16given(-0.329173, 0.379945, -0.864458), (0.796919, 0.602858, -0.038488), (0.506522, -0.701572, -0.50123)-52.373562, 42.406849, -122.738564
17given(1), (1), (1)
18given(-0.384335, 0.447571, -0.807445), (-0.789533, -0.612638, 0.036221), (-0.47846, 0.651425, 0.58883)-42.718609, -72.819763, 65.260307
19given(1), (1), (1)
20given(-0.232045, -0.370012, 0.899581), (0.812964, -0.581566, -0.029505), (0.534083, 0.724481, 0.435756)76.590363, -14.28892, 28.601971
21given(1), (1), (1)
22given(-0.285363, -0.453918, 0.844112), (-0.813873, 0.579883, 0.036689), (-0.50614, -0.676531, -0.534909)69.278214, -14.54181, -98.933144
23given(1), (1), (1)
24given(-0.998183, 0.030966, 0.051686), (-0.002679, -0.879789, 0.475357), (0.060192, 0.474355, 0.878274)3.60978, -12.07102, 73.452797
25given(1), (1), (1)
26given(-0.99362, 0.025701, -0.109811), (0.075679, 0.873863, -0.480246), (0.083617, -0.485492, -0.870233)-11.71079, -18.87915, -134.599579
27given(1), (1), (1)
28given(-0.012886, 0.634333, 0.772953), (-0.626913, 0.597091, -0.500462), (-0.778983, -0.491023, 0.389977)39.49395, 10.26837, -43.279362
29given(1), (1), (1)
30given(-0.100691, -0.674797, -0.731102), (-0.603784, -0.542605, 0.583973), (-0.790763, 0.500229, -0.352796)-24.848261, 25.46814, -51.988319
31given(1), (1), (1)
32given(0.037649, -0.703646, -0.709552), (0.605893, 0.580723, -0.543741), (0.794655, -0.409441, 0.448198)-24.159161, -54.315159, -6.44318
33given(1), (1), (1)
34given(0.118771, 0.658178, 0.743435), (0.62078, -0.63358, 0.461746), (0.774936, 0.406667, -0.483834)39.20779, -42.594582, -23.44206
35given(1), (1), (1)
36given(-0.413749, 0.448655, -0.792162), (-0.785941, -0.615177, 0.062083), (-0.459466, 0.648279, 0.607145)-41.855289, -70.961929, 66.752724
37given(1), (1), (1)
38given(-0.29659, 0.378212, -0.876921), (0.800002, 0.59988, -0.011849), (0.521566, -0.705053, -0.480489)-52.94722, 44.271351, -121.117363
39given(1), (1), (1)
40given(-0.321576, -0.442372, 0.837195), (-0.804715, 0.593644, 0.00458), (-0.499022, -0.672231, -0.546885)68.362762, -17.6444, -99.857246
41given(1), (1), (1)
42given(-0.193383, -0.380503, 0.904334), (0.821808, -0.56632, -0.062546), (0.535942, 0.731094, 0.422218)77.407021, -17.476339, 27.524389
43given(1), (1), (1)
44given(0.996646, -0.057267, 0.058456), (-0.05774, -0.998311, 0.006441), (0.057989, -0.009795, -0.998269)2.77827, -93.161171, -186.759979
45given(1), (1), (1)
46given(-0.03217, -0.664431, -0.746657), (0.182067, -0.73844, 0.649275), (-0.98276, -0.115055, 0.144727)-42.905041, -73.905647, -90.064659
47given(1), (1), (1)
48given(0.055152, 0.705717, 0.706344), (0.154069, 0.692933, -0.704348), (-0.98652, 0.147672, -0.070513)20.725691, -93.409233, -93.834213
49given(1), (1), (1)
50given(0.008859, 0.676145, 0.736715), (-0.155359, -0.726867, 0.668975), (0.987818, -0.120382, 0.098605)23.019609, -1.58895, -91.671066
51given(1), (1), (1)
52given(-0.073841, -0.630754, -0.772462), (-0.175253, 0.77073, -0.612586), (0.98175, 0.090142, -0.167453)-41.275982, -17.99498, -97.768806
53given(1), (1), (1)
54given(0.387321, -0.407421, 0.827037), (0.461102, 0.862407, 0.208901), (-0.798353, 0.300437, 0.521891)45.110378, 47.218208, -36.192139
55given(1), (1), (1)
56given(0.322699, -0.423092, 0.846675), (-0.468778, -0.848554, -0.245363), (0.822261, -0.317724, -0.472164)44.49276, -143.524719, -147.212723
57given(1), (1), (1)
58given(0.291623, 0.399306, -0.869201), (0.46224, -0.854382, -0.237414), (-0.837431, -0.332544, -0.433732)-75.158653, -75.255493, -151.426208
59given(1), (1), (1)
60given(0.221254, 0.426985, -0.876773), (-0.478188, 0.831055, 0.28405), (0.849931, 0.356415, 0.388053)-76.36348, -14.69936, -39.03511
61given(1), (1), (1)
62given(-0.099839, -0.626926, -0.772655), (-0.168178, 0.775995, -0.607904), (0.980688, 0.069251, -0.18291)-41.053299, -17.58007, -99.147217
63given(1), (1), (1)
64given(-0.011306, 0.672081, 0.740392), (-0.146496, -0.733563, 0.663645), (0.989147, -0.100961, 0.106751)23.28063, -1.67457, -91.746109
65given(1), (1), (1)
66given(0.075365, 0.707063, 0.703124), (0.140293, 0.690597, -0.709503), (-0.987238, 0.152114, -0.047149)20.526739, -93.40197, -92.886803
67given(1), (1), (1)
68given(-0.006612, -0.668304, -0.743859), (0.169782, -0.733825, 0.65778), (-0.98546, -0.121945, 0.118318)-43.097881, -73.359009, -90.92762
69given(1), (1), (1)
70given(0.313274, -0.438275, 0.842481), (-0.473853, -0.84095, -0.261277), (0.822996, -0.317361, -0.471126)42.835911, -144.067032, -146.835571
71given(1), (1), (1)
72given(0.39648, -0.390927, 0.83065), (0.4405, 0.874853, 0.201474), (-0.805459, 0.286021, 0.519065)46.79541, 47.569809, -37.46006
73given(1), (1), (1)
74given(0.215799, 0.428833, -0.877231), (-0.47046, 0.832907, 0.291432), (0.855627, 0.349812, 0.381489)-76.58802, -13.72942, -39.636742
75given(1), (1), (1)
76given(0.29661, 0.398025, -0.8681), (0.455639, -0.857856, -0.237646), (-0.839294, -0.325052, -0.435805)-74.874687, -75.292641, -151.493866
77given(1), (1), (1)
78given(0.995793, -0.041056, -0.081913), (-0.036312, -0.997622, 0.058583), (-0.084123, -0.055363, -0.994916)-1.91329, -27.450121, -60.72863
79given(1), (1), (1)
80given(-0.999255, -0.038384, 0.003923), (-0.007896, 0.103924, -0.994554), (0.037768, -0.993844, -0.10415)12.81047, -97.006157, -2.68751
81given(1), (1), (1)
82given(-0.99435, 0.071803, 0.078186), (0.065852, -0.160456, 0.984844), (0.083261, 0.984428, 0.154821)17.690201, -41.49107, 33.970921
83given(1), (1), (1)
84given(0.856109, -0.124734, -0.501516), (-0.505855, -0.400873, -0.763814), (-0.105771, 0.907602, -0.406289)-33.69566, -154.130615, 20.713051
85given(1), (1), (1)
86given(-0.903926, 0.169829, 0.392526), (0.035474, 0.944391, -0.326906), (-0.426216, -0.281575, -0.859683)40.587608, -0.06019, -118.760178
87given(1), (1), (1)
88given(0.897311, 0.158055, 0.41213), (-0.439648, 0.403094, 0.802636), (-0.039266, -0.901407, 0.431189)61.18903, 29.44417, 14.20877
89given(1), (1), (1)
90given(-0.92981, -0.211455, -0.301231), (0.106948, -0.938392, 0.328606), (-0.352159, 0.273325, 0.895141)-38.261002, -27.319071, 70.813057
91given(1), (1), (1)
92given(-0.997937, 0.042901, 0.047761), (0.045792, -0.045763, 0.997902), (0.044997, 0.998031, 0.043704)12.22714, 65.580322, -63.116161
93given(1), (1), (1)
94given(-0.999574, -0.005238, 0.028718), (-0.029104, 0.102218, -0.994336), (0.002272, -0.994748, -0.102327)12.07324, 7.93124, -96.638359
95given(1), (1), (1)
96given(0.879703, -0.186114, -0.43759), (0.475495, 0.354467, 0.805144), (0.005263, -0.91636, 0.400322)-33.917141, 123.154831, -85.877678
97given(1), (1), (1)
98given(-0.86559, 0.158297, 0.475074), (0.025394, -0.933623, 0.357356), (0.500108, 0.321388, 0.804115)46.194321, -25.87759, 55.858639
99given(1), (1), (1)
100given(0.913078, 0.218112, 0.344553), (0.403352, -0.358806, -0.841763), (-0.059971, 0.907571, -0.415594)54.42387, -63.538601, -76.372993
101given(1), (1), (1)
102given(-0.900171, -0.19908, -0.387375), (-0.048822, 0.929937, -0.364463), (0.432791, -0.309167, -0.846822)-47.275059, -5.85769, -127.892563
103given(1), (1), (1)
104given(0.996354, -0.035992, -0.077355), (-0.040459, -0.997555, -0.056988), (-0.075115, 0.05991, -0.995374)-4.03523, -30.819651, -58.93116
105given(1), (1), (1)
106given(-0.855741, 0.161301, 0.49162), (0.020528, -0.938832, 0.343764), (0.516998, 0.304265, 0.800085)47.712952, -27.360229, 54.209049
107given(1), (1), (1)
108given(0.887738, -0.185222, -0.421444), (0.460301, 0.370448, 0.806778), (0.00669, -0.910198, 0.414119)-32.63908, 124.411667, -84.473808
109given(1), (1), (1)
110given(-0.8965, -0.191399, -0.399567), (-0.03714, 0.931161, -0.362711), (0.441484, -0.310331, -0.841895)-48.467312, -5.59385, -127.507507
111given(1), (1), (1)
112given(0.915931, 0.226187, 0.331528), (0.394858, -0.360049, -0.845252), (-0.071819, 0.905099, -0.419092)53.153728, -63.957039, -76.942467
113given(1), (1), (1)
114given(-0.893308, 0.173735, 0.414508), (0.038964, 0.94873, -0.313676), (-0.447753, -0.264058, -0.854278)42.61758, 1.3149, -117.002579
115given(1), (1), (1)
116given(0.865544, -0.130568, -0.483514), (-0.490485, -0.416217, -0.765629), (-0.10128, 0.899842, -0.424296)-32.80286, -155.335709, 18.952789
117given(1), (1), (1)
118given(-0.924568, -0.205794, -0.320659), (0.096232, -0.940431, 0.326082), (-0.368663, 0.270627, 0.889296)-40.18924, -27.62015, 70.203506
119given(1), (1), (1)
120given(0.902134, 0.171203, 0.396036), (-0.430911, 0.403672, 0.807072), (-0.021696, -0.898743, 0.437939)59.670841, 29.98218, 15.21114
121given(1), (1), (1)
122given(-0.746757, -0.302973, 0.592082), (-0.288094, -0.65502, -0.698535), (0.599462, -0.692211, 0.401856)0.36104, -197.627258, -98.291847
123given(1), (1), (1)
124given(0.994741, 0.025525, -0.099187), (0.02751, -0.999447, 0.01869), (-0.098655, -0.02132, -0.994893)-11.00028, -91.303497, -185.171509
125given(1), (1), (1)
126given(-0.813104, 0.265436, -0.518078), (-0.246221, 0.649633, 0.719272), (0.527481, 0.712405, -0.462863)-73.273888, -4.72043, -114.836388
127given(1), (1), (1)
128given(-0.810067, 0.255851, -0.527572), (-0.250876, 0.662011, 0.706259), (0.529956, 0.704472, -0.472086)-74.221336, -6.0902, -115.959991
129given(1), (1), (1)
130given(0.994356, 0.041482, -0.097654), (0.042371, -0.999077, 0.007047), (-0.097271, -0.011145, -0.995196)-10.49731, -92.517967, -185.011292
131given(1), (1), (1)
132given(-0.86749, 0.211481, -0.450264), (0.21385, -0.658691, -0.721384), (-0.449144, -0.722082, 0.526182)-66.54425, -89.553093, -62.073631

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Components

#1: Protein
Phosphoserine aminotransferase / Phosphoserine aminotransferase / putative


Mass: 40584.965 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EhPSAT, EHI_026360 / Plasmid: pET21C / Production host: Escherichia coli (E. coli) / References: UniProt: Q60I38, phosphoserine transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.37 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25-30% PEG 3350 (w/v), 100 mM Tris pH 6.5, 200mM sodium formate, 5 % glycerol (v/v)

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 10, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.888
11H, H-K, -L20.112
ReflectionResolution: 2.94→50.15 Å / Num. obs: 76771 / % possible obs: 94.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.083 / Rsym value: 0.051 / Net I/σ(I): 14.911
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.881 / % possible all: 85.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data collection
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BT4
Resolution: 2.94→50.15 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.862 / SU B: 42.403 / SU ML: 0.389 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.301 3764 4.9 %RANDOM
Rwork0.265 ---
obs0.267 73001 87.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 76.93 Å2
Baniso -1Baniso -2Baniso -3
1-9.03 Å2-37.97 Å223.05 Å2
2---6.13 Å28.3 Å2
3----2.91 Å2
Refinement stepCycle: LAST / Resolution: 2.94→50.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27082 0 165 155 27402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01927656
X-RAY DIFFRACTIONr_bond_other_d0.0080.0225136
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.96737611
X-RAY DIFFRACTIONr_angle_other_deg1.091357361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.33353849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52625.109873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.187154088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8111568
X-RAY DIFFRACTIONr_chiral_restr0.0830.24485
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0232192
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025782
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1601tight positional0.130.17
1A1221tight positional0.10.17
1A3213tight positional0.130.17
1A3076tight positional0.130.17
1A2845tight positional0.120.17
1A2599tight positional0.170.17
1A2891tight positional0.150.17
1A2354tight positional0.150.17
1A2426tight positional0.120.17
1A1480tight positional0.120.17
2A1601tight positional0.120.17
2A1221tight positional0.110.17
2A3074tight positional0.110.17
2A2835tight positional0.110.17
2A2599tight positional0.160.17
2A2881tight positional0.130.17
2A2354tight positional0.130.17
2A2416tight positional0.090.17
2A1480tight positional0.090.17
2A1601tight positional0.130.17
3A1221tight positional0.10.17
3A2790tight positional0.220.17
3A2567tight positional0.150.17
3A2822tight positional0.30.17
3A2333tight positional0.120.17
3A2362tight positional0.090.17
3A1469tight positional0.10.17
3A1580tight positional0.120.17
3A1215tight positional0.090.17
3A2536tight positional0.150.17
4A2686tight positional0.290.17
4A2248tight positional0.120.17
4A2262tight positional0.080.17
4A1471tight positional0.10.17
4A1546tight positional0.120.17
4A1212tight positional0.10.17
4A2435tight positional0.140.17
4A2094tight positional0.160.17
4A2096tight positional0.140.17
4A1480tight positional0.110.17
5A1429tight positional0.180.17
5A1221tight positional0.090.17
5A2209tight positional0.160.17
5A2308tight positional0.250.17
5A1407tight positional0.10.17
5A1564tight positional0.150.17
5A1177tight positional0.080.17
5A2012tight positional0.10.17
5A1387tight positional0.120.17
5A1525tight positional0.140.17
6A1168tight positional0.110.17
6A1418tight positional0.090.17
6A1424tight positional0.080.17
6A1178tight positional0.080.17
6A1023tight positional0.080.17
6A1141tight positional0.10.17
6A990tight positional0.090.17
1A3279tight thermal4.611.66
2A3188tight thermal5.971.66
3A3061tight thermal5.581.66
4A2830tight thermal5.331.66
5A2593tight thermal7.371.66
6A2876tight thermal9.111.66
7A2338tight thermal6.91.66
8A2411tight thermal7.361.66
9A1480tight thermal5.781.66
10A1601tight thermal12.651.66
11A1221tight thermal11.591.66
12B3213tight thermal5.391.66
13B3076tight thermal5.461.66
14B2845tight thermal5.11.66
15B2599tight thermal6.811.66
16B2891tight thermal8.681.66
17B2354tight thermal7.761.66
18B2426tight thermal7.231.66
19B1480tight thermal5.281.66
20B1601tight thermal11.821.66
21B1221tight thermal10.961.66
22C3074tight thermal5.381.66
23C2835tight thermal5.431.66
24C2599tight thermal5.211.66
25C2881tight thermal6.951.66
26C2354tight thermal9.051.66
27C2416tight thermal6.221.66
28C1480tight thermal5.731.66
29C1601tight thermal10.21.66
30C1221tight thermal9.371.66
31D2790tight thermal5.951.66
32D2567tight thermal5.841.66
33D2822tight thermal81.66
34D2333tight thermal8.761.66
35D2362tight thermal6.681.66
36D1469tight thermal5.971.66
37D1580tight thermal11.691.66
38D1215tight thermal10.191.66
39E2536tight thermal6.651.66
40E2686tight thermal8.271.66
41E2248tight thermal6.721.66
42E2262tight thermal7.181.66
43E1471tight thermal4.781.66
44E1546tight thermal11.761.66
45E1212tight thermal10.741.66
46F2435tight thermal5.671.66
47F2094tight thermal10.621.66
48F2096tight thermal6.641.66
49F1480tight thermal6.471.66
50F1429tight thermal8.871.66
51F1221tight thermal7.641.66
52G2209tight thermal12.411.66
53G2308tight thermal7.281.66
54G1407tight thermal8.671.66
55G1564tight thermal7.441.66
56G1177tight thermal6.271.66
57H2012tight thermal10.351.66
58H1387tight thermal6.951.66
59H1525tight thermal15.711.66
60H1168tight thermal14.071.66
61I1418tight thermal8.251.66
62I1424tight thermal11.181.66
63I1178tight thermal9.071.66
64J1023tight thermal13.071.66
65J1141tight thermal10.631.66
66K990tight thermal8.041.66
LS refinement shellResolution: 2.94→3.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 19 -
Rwork0.272 515 -
obs--8.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.34360.07850.43331.5958-0.23242.8989-0.02120.1488-0.1079-0.27750.09610.1087-0.0145-0.206-0.07490.27190.1514-0.10450.1657-0.07320.0666-12.6961-20.2716-45.9012
21.43120.2053-0.11762.06810.18613.02810.0905-0.18260.15820.3851-0.01110.0764-0.3698-0.1125-0.07940.37660.1821-0.00880.1592-0.0640.0715-10.5102-9.2821-14.592
31.61491.27370.50223.69211.85782.50120.0942-0.33580.00210.3396-0.14470.08970.07350.2790.05060.13540.0702-0.04830.3192-0.07010.03978.6225-45.1011-76.925
41.55510.97770.48513.27061.35272.585-0.4620.27760.0962-1.24470.59420.1614-0.64340.4766-0.13220.589-0.1244-0.10390.4432-0.08930.10769.1026-48.8812-108.7573
51.67960.9195-0.15143.2184-1.52753.80910.1426-0.168-0.38980.32940.00350.1225-0.2972-0.1928-0.14620.24010.1592-0.10110.25490.0710.2775-9.1253-55.7417-18.5853
62.29920.57680.1622.2636-0.70073.6167-0.0423-0.0530.5802-0.25840.0830.2970.2487-0.5119-0.04070.21920.1112-0.06120.2094-0.00580.1849-8.957424.1518-42.4297
72.30830.17811.8342.4014-1.17173.2222-0.04490.43170.3688-0.1723-0.4764-0.45580.10751.1140.52120.1930.21440.09620.57340.22380.192621.682220.2516-38.2688
82.39271.2833-1.23052.5737-1.75732.12220.039-0.2165-0.77940.1957-0.6475-0.7846-0.13011.17160.60850.46060.072-0.39431.0270.22330.753120.7068-51.4708-25.3582
92.50860.2734-1.46222.1655-0.40123.1003-0.39540.27220.152-0.45350.27430.70610.5004-0.5120.12110.448-0.0418-0.24640.41520.04370.5311-23.6047-77.3737-70.399
103.27921.3639-2.35763.392-1.66462.0878-0.81090.1927-0.4927-1.03710.4362-0.13070.83170.09540.37481.03730.0625-0.04260.5215-0.01710.2313-1.7038-83.0144-85.928
112.4609-0.80270.00083.10441.5884.04870.1476-0.2524-0.0209-0.4198-0.34250.7962-0.4593-0.56240.19490.53160.0381-0.31040.2053-0.0550.3563-24.5984-18.7136-110.9696
124.48120.16861.31634.61860.82722.3075-0.0713-0.47720.47280.1120.2019-0.5844-0.33210.5002-0.13060.6236-0.1289-0.15910.4414-0.0880.2422-1.1278-11.7194-96.525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 354
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION1A501 - 514
4X-RAY DIFFRACTION2B6 - 354
5X-RAY DIFFRACTION2B401 - 402
6X-RAY DIFFRACTION2B501 - 512
7X-RAY DIFFRACTION3C6 - 354
8X-RAY DIFFRACTION3C401 - 402
9X-RAY DIFFRACTION3C501 - 516
10X-RAY DIFFRACTION4D6 - 354
11X-RAY DIFFRACTION4D401 - 402
12X-RAY DIFFRACTION4D501 - 511
13X-RAY DIFFRACTION5E6 - 353
14X-RAY DIFFRACTION5E401 - 402
15X-RAY DIFFRACTION5E501 - 518
16X-RAY DIFFRACTION6F6 - 348
17X-RAY DIFFRACTION6F401
18X-RAY DIFFRACTION6F501 - 509
19X-RAY DIFFRACTION7G6 - 354
20X-RAY DIFFRACTION7G401
21X-RAY DIFFRACTION7G501 - 513
22X-RAY DIFFRACTION8H6 - 354
23X-RAY DIFFRACTION8H401
24X-RAY DIFFRACTION8H501 - 519
25X-RAY DIFFRACTION9I6 - 354
26X-RAY DIFFRACTION9I401
27X-RAY DIFFRACTION9I501 - 523
28X-RAY DIFFRACTION10J9 - 261
29X-RAY DIFFRACTION10J401 - 410
30X-RAY DIFFRACTION11K38 - 353
31X-RAY DIFFRACTION11K401
32X-RAY DIFFRACTION11K501 - 508
33X-RAY DIFFRACTION12L35 - 250
34X-RAY DIFFRACTION12L401 - 402

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About Yorodumi

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

New format data for meta-information of EMDB entries

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