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- PDB-7kel: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant w... -

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基本情報

登録情報
データベース: PDB / ID: 7kel
タイトルDihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site
要素4-hydroxy-tetrahydrodipicolinate synthase
キーワードLYASE / DIHYDRODIPICOLINATE SYNTHASE
機能・相同性
機能・相同性情報


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
類似検索 - 分子機能
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
類似検索 - ドメイン・相同性
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
類似検索 - 構成要素
生物種Campylobacter jejuni (カンピロバクター)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.1 Å
データ登録者Saran, S. / Sanders, D.A.R.
資金援助 カナダ, 1件
組織認可番号国
Natural Sciences and Engineering Research Council (NSERC, Canada) カナダ
引用ジャーナル: To Be Published
タイトル: Reversing the roles of a crucial hydrogen-bonding pair: a lysine-insensitive mutant of Campylobacter jejuni dihydrodipicolinate synthase, H59K, binds histidine in its allosteric site
著者: Yazdi, M.M. / Saran, S. / Sanders, D.A.R. / Palmer, D.R.J.
履歴
登録2020年10月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年10月13日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22023年11月29日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
I: 4-hydroxy-tetrahydrodipicolinate synthase
J: 4-hydroxy-tetrahydrodipicolinate synthase
K: 4-hydroxy-tetrahydrodipicolinate synthase
L: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)417,274112
ポリマ－410,11612
非ポリマー7,158100
水28,3201572
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,62922
ポリマ－68,3532
非ポリマー1,27720
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-1 kcal/mol
Surface area21900 Å2
手法PISA
2
C: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,94524
ポリマ－68,3532
非ポリマー1,59222
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint15 kcal/mol
Surface area22170 Å2
手法PISA
3
D: 4-hydroxy-tetrahydrodipicolinate synthase
G: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,22214
ポリマ－68,3532
非ポリマー86912
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-8 kcal/mol
Surface area22450 Å2
手法PISA
4
E: 4-hydroxy-tetrahydrodipicolinate synthase
K: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,19214
ポリマ－68,3532
非ポリマー83912
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-26 kcal/mol
Surface area22550 Å2
手法PISA
5
H: 4-hydroxy-tetrahydrodipicolinate synthase
J: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,56619
ポリマ－68,3532
非ポリマー1,21317
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-4 kcal/mol
Surface area21380 Å2
手法PISA
6
I: 4-hydroxy-tetrahydrodipicolinate synthase
L: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,72019
ポリマ－68,3532
非ポリマー1,36717
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint5 kcal/mol
Surface area21940 Å2
手法PISA
単位格子
Length a, b, c (Å)82.880, 201.440, 113.660
Angle α, β, γ (deg.)90.000, 108.450, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 5:17 or resid 19:20 or resid...
21(chain B and (resid 5:17 or resid 19:20 or resid...
31(chain C and (resid 5:17 or resid 19:20 or resid...
41(chain D and (resid 5:17 or resid 19:20 or resid...
51(chain E and (resid 5:17 or resid 19:20 or resid...
61(chain F and (resid 5:17 or resid 19:20 or resid...
71(chain G and (resid 5:17 or resid 19:20 or resid...
81(chain H and (resid 5:17 or resid 19:20 or resid...
91(chain I and (resid 5:17 or resid 19:20 or resid...
101(chain J and (resid 5:17 or resid 19:20 or resid...
111(chain K and (resid 5:17 or resid 19:20 or resid...
121(chain L and (resid 5:17 or resid 19:20 or resid...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5:17 or resid 19:20 or resid...A5 - 17
121(chain A and (resid 5:17 or resid 19:20 or resid...A19 - 20
131(chain A and (resid 5:17 or resid 19:20 or resid...A22 - 24
141(chain A and (resid 5:17 or resid 19:20 or resid...A26 - 28
151(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 31
161(chain A and (resid 5:17 or resid 19:20 or resid...A33 - 55
171(chain A and (resid 5:17 or resid 19:20 or resid...A58 - 59
181(chain A and (resid 5:17 or resid 19:20 or resid...A61 - 67
191(chain A and (resid 5:17 or resid 19:20 or resid...A69 - 70
1101(chain A and (resid 5:17 or resid 19:20 or resid...A72 - 73
1111(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1121(chain A and (resid 5:17 or resid 19:20 or resid...A78 - 86
1131(chain A and (resid 5:17 or resid 19:20 or resid...A86 - 94
1141(chain A and (resid 5:17 or resid 19:20 or resid...A99 - 97
1151(chain A and (resid 5:17 or resid 19:20 or resid...A91 - 127
1161(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1171(chain A and (resid 5:17 or resid 19:20 or resid...A167 - 183
1181(chain A and (resid 5:17 or resid 19:20 or resid...A236 - 264
1191(chain A and (resid 5:17 or resid 19:20 or resid...A236 - 266
1201(chain A and (resid 5:17 or resid 19:20 or resid...A268 - 279
1211(chain A and (resid 5:17 or resid 19:20 or resid...A282 - 287
1221(chain A and (resid 5:17 or resid 19:20 or resid...A293
1231(chain A and (resid 5:17 or resid 19:20 or resid...A298
1241(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1251(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1261(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1271(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1281(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1291(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1301(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1311(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1321(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
211(chain B and (resid 5:17 or resid 19:20 or resid...B5 - 17
221(chain B and (resid 5:17 or resid 19:20 or resid...B19 - 20
231(chain B and (resid 5:17 or resid 19:20 or resid...B22 - 24
241(chain B and (resid 5:17 or resid 19:20 or resid...B26 - 28
251(chain B and (resid 5:17 or resid 19:20 or resid...B33 - 55
261(chain B and (resid 5:17 or resid 19:20 or resid...B58 - 59
271(chain B and (resid 5:17 or resid 19:20 or resid...B61 - 67
281(chain B and (resid 5:17 or resid 19:20 or resid...B69 - 70
291(chain B and (resid 5:17 or resid 19:20 or resid...B72 - 73
2101(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2111(chain B and (resid 5:17 or resid 19:20 or resid...B88 - 86
2121(chain B and (resid 5:17 or resid 19:20 or resid...B96 - 94
2131(chain B and (resid 5:17 or resid 19:20 or resid...B99 - 97
2141(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
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2161(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2171(chain B and (resid 5:17 or resid 19:20 or resid...B167 - 183
2181(chain B and (resid 5:17 or resid 19:20 or resid...B185 - 230
2191(chain B and (resid 5:17 or resid 19:20 or resid...B236 - 266
2201(chain B and (resid 5:17 or resid 19:20 or resid...B268 - 27
2211(chain B and (resid 5:17 or resid 19:20 or resid...B282 - 287
2221(chain B and (resid 5:17 or resid 19:20 or resid...B289 - 290
2231(chain B and (resid 5:17 or resid 19:20 or resid...B293
2241(chain B and (resid 5:17 or resid 19:20 or resid...B295 - 297
2251(chain B and (resid 5:17 or resid 19:20 or resid...B298
2261(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2271(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2281(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2291(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2301(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2311(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2321(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
311(chain C and (resid 5:17 or resid 19:20 or resid...C5 - 17
321(chain C and (resid 5:17 or resid 19:20 or resid...C19 - 20
331(chain C and (resid 5:17 or resid 19:20 or resid...C22 - 24
341(chain C and (resid 5:17 or resid 19:20 or resid...C26 - 28
351(chain C and (resid 5:17 or resid 19:20 or resid...C33 - 55
361(chain C and (resid 5:17 or resid 19:20 or resid...C58 - 59
371(chain C and (resid 5:17 or resid 19:20 or resid...C61 - 67
381(chain C and (resid 5:17 or resid 19:20 or resid...C69 - 70
391(chain C and (resid 5:17 or resid 19:20 or resid...C72 - 73
3101(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3111(chain C and (resid 5:17 or resid 19:20 or resid...C88 - 86
3121(chain C and (resid 5:17 or resid 19:20 or resid...C96 - 94
3131(chain C and (resid 5:17 or resid 19:20 or resid...C99 - 97
3141(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3151(chain C and (resid 5:17 or resid 19:20 or resid...C161 - 165
3161(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3171(chain C and (resid 5:17 or resid 19:20 or resid...C167 - 183
3181(chain C and (resid 5:17 or resid 19:20 or resid...C185 - 230
3191(chain C and (resid 5:17 or resid 19:20 or resid...C236 - 266
3201(chain C and (resid 5:17 or resid 19:20 or resid...C268 - 27
3211(chain C and (resid 5:17 or resid 19:20 or resid...C282 - 287
3221(chain C and (resid 5:17 or resid 19:20 or resid...C289 - 290
3231(chain C and (resid 5:17 or resid 19:20 or resid...C293
3241(chain C and (resid 5:17 or resid 19:20 or resid...C295 - 297
3251(chain C and (resid 5:17 or resid 19:20 or resid...C298
3261(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3271(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3281(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3291(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3301(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3311(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3321(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
411(chain D and (resid 5:17 or resid 19:20 or resid...D5 - 17
421(chain D and (resid 5:17 or resid 19:20 or resid...D19 - 20
431(chain D and (resid 5:17 or resid 19:20 or resid...D22 - 24
441(chain D and (resid 5:17 or resid 19:20 or resid...D33 - 55
451(chain D and (resid 5:17 or resid 19:20 or resid...D4 - 31
461(chain D and (resid 5:17 or resid 19:20 or resid...D58 - 59
471(chain D and (resid 5:17 or resid 19:20 or resid...D4 - 67
481(chain D and (resid 5:17 or resid 19:20 or resid...D69 - 70
491(chain D and (resid 5:17 or resid 19:20 or resid...D0
4101(chain D and (resid 5:17 or resid 19:20 or resid...D4 - 298
4111(chain D and (resid 5:17 or resid 19:20 or resid...D77 - 86
4121(chain D and (resid 5:17 or resid 19:20 or resid...D96 - 97
4131(chain D and (resid 5:17 or resid 19:20 or resid...D99
4141(chain D and (resid 5:17 or resid 19:20 or resid...D129 - 159
4151(chain D and (resid 5:17 or resid 19:20 or resid...D167 - 183
4161(chain D and (resid 5:17 or resid 19:20 or resid...D185 - 2
4171(chain D and (resid 5:17 or resid 19:20 or resid...D2330
4181(chain D and (resid 5:17 or resid 19:20 or resid...D4 - 298
4191(chain D and (resid 5:17 or resid 19:20 or resid...D282 - 287
4201(chain D and (resid 5:17 or resid 19:20 or resid...D293
4211(chain D and (resid 5:17 or resid 19:20 or resid...D295 - 2
511(chain E and (resid 5:17 or resid 19:20 or resid...E5 - 17
521(chain E and (resid 5:17 or resid 19:20 or resid...E19 - 20
531(chain E and (resid 5:17 or resid 19:20 or resid...E22 - 24
541(chain E and (resid 5:17 or resid 19:20 or resid...E26 - 28
551(chain E and (resid 5:17 or resid 19:20 or resid...E33 - 55
561(chain E and (resid 5:17 or resid 19:20 or resid...E58 - 59
571(chain E and (resid 5:17 or resid 19:20 or resid...E61 - 67
581(chain E and (resid 5:17 or resid 19:20 or resid...E69 - 70
591(chain E and (resid 5:17 or resid 19:20 or resid...E72 - 73
5101(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5111(chain E and (resid 5:17 or resid 19:20 or resid...E88 - 86
5121(chain E and (resid 5:17 or resid 19:20 or resid...E96 - 94
5131(chain E and (resid 5:17 or resid 19:20 or resid...E99 - 97
5141(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5151(chain E and (resid 5:17 or resid 19:20 or resid...E161 - 165
5161(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5171(chain E and (resid 5:17 or resid 19:20 or resid...E167 - 183
5181(chain E and (resid 5:17 or resid 19:20 or resid...E185 - 230
5191(chain E and (resid 5:17 or resid 19:20 or resid...E236 - 266
5201(chain E and (resid 5:17 or resid 19:20 or resid...E268 - 27
5211(chain E and (resid 5:17 or resid 19:20 or resid...E282 - 287
5221(chain E and (resid 5:17 or resid 19:20 or resid...E289 - 290
5231(chain E and (resid 5:17 or resid 19:20 or resid...E293
5241(chain E and (resid 5:17 or resid 19:20 or resid...E295 - 297
5251(chain E and (resid 5:17 or resid 19:20 or resid...E298
5261(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
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5281(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5291(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5301(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5311(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5321(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
611(chain F and (resid 5:17 or resid 19:20 or resid...F5 - 17
621(chain F and (resid 5:17 or resid 19:20 or resid...F19 - 20
631(chain F and (resid 5:17 or resid 19:20 or resid...F22 - 24
641(chain F and (resid 5:17 or resid 19:20 or resid...F33 - 55
651(chain F and (resid 5:17 or resid 19:20 or resid...F3 - 31
661(chain F and (resid 5:17 or resid 19:20 or resid...F58 - 59
671(chain F and (resid 5:17 or resid 19:20 or resid...F3 - 67
681(chain F and (resid 5:17 or resid 19:20 or resid...F69 - 70
691(chain F and (resid 5:17 or resid 19:20 or resid...F0
6101(chain F and (resid 5:17 or resid 19:20 or resid...F3 - 298
6111(chain F and (resid 5:17 or resid 19:20 or resid...F77 - 86
6121(chain F and (resid 5:17 or resid 19:20 or resid...F96 - 97
6131(chain F and (resid 5:17 or resid 19:20 or resid...F99
6141(chain F and (resid 5:17 or resid 19:20 or resid...F129 - 159
6151(chain F and (resid 5:17 or resid 19:20 or resid...F167 - 183
6161(chain F and (resid 5:17 or resid 19:20 or resid...F185 - 2
6171(chain F and (resid 5:17 or resid 19:20 or resid...F2330
6181(chain F and (resid 5:17 or resid 19:20 or resid...F3 - 298
6191(chain F and (resid 5:17 or resid 19:20 or resid...F282 - 287
6201(chain F and (resid 5:17 or resid 19:20 or resid...F293
6211(chain F and (resid 5:17 or resid 19:20 or resid...F295 - 2
711(chain G and (resid 5:17 or resid 19:20 or resid...G5 - 17
721(chain G and (resid 5:17 or resid 19:20 or resid...G19 - 20
731(chain G and (resid 5:17 or resid 19:20 or resid...G22 - 24
741(chain G and (resid 5:17 or resid 19:20 or resid...G33 - 55
751(chain G and (resid 5:17 or resid 19:20 or resid...G3 - 31
761(chain G and (resid 5:17 or resid 19:20 or resid...G58 - 59
771(chain G and (resid 5:17 or resid 19:20 or resid...G3 - 67
781(chain G and (resid 5:17 or resid 19:20 or resid...G69 - 70
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7101(chain G and (resid 5:17 or resid 19:20 or resid...G3 - 298
7111(chain G and (resid 5:17 or resid 19:20 or resid...G77 - 86
7121(chain G and (resid 5:17 or resid 19:20 or resid...G96 - 97
7131(chain G and (resid 5:17 or resid 19:20 or resid...G99
7141(chain G and (resid 5:17 or resid 19:20 or resid...G129 - 159
7151(chain G and (resid 5:17 or resid 19:20 or resid...G167 - 183
7161(chain G and (resid 5:17 or resid 19:20 or resid...G185 - 2
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7181(chain G and (resid 5:17 or resid 19:20 or resid...G3 - 298
7191(chain G and (resid 5:17 or resid 19:20 or resid...G282 - 287
7201(chain G and (resid 5:17 or resid 19:20 or resid...G293
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821(chain H and (resid 5:17 or resid 19:20 or resid...H19 - 20
831(chain H and (resid 5:17 or resid 19:20 or resid...H22 - 24
841(chain H and (resid 5:17 or resid 19:20 or resid...H33 - 55
851(chain H and (resid 5:17 or resid 19:20 or resid...H3 - 31
861(chain H and (resid 5:17 or resid 19:20 or resid...H58 - 59
871(chain H and (resid 5:17 or resid 19:20 or resid...H3 - 67
881(chain H and (resid 5:17 or resid 19:20 or resid...H69 - 70
891(chain H and (resid 5:17 or resid 19:20 or resid...H0
8101(chain H and (resid 5:17 or resid 19:20 or resid...H3 - 298
8111(chain H and (resid 5:17 or resid 19:20 or resid...H77 - 86
8121(chain H and (resid 5:17 or resid 19:20 or resid...H96 - 97
8131(chain H and (resid 5:17 or resid 19:20 or resid...H99
8141(chain H and (resid 5:17 or resid 19:20 or resid...H129 - 159
8151(chain H and (resid 5:17 or resid 19:20 or resid...H167 - 183
8161(chain H and (resid 5:17 or resid 19:20 or resid...H185 - 2
8171(chain H and (resid 5:17 or resid 19:20 or resid...H2330
8181(chain H and (resid 5:17 or resid 19:20 or resid...H3 - 298
8191(chain H and (resid 5:17 or resid 19:20 or resid...H282 - 287
8201(chain H and (resid 5:17 or resid 19:20 or resid...H293
8211(chain H and (resid 5:17 or resid 19:20 or resid...H295 - 2
911(chain I and (resid 5:17 or resid 19:20 or resid...I5 - 17
921(chain I and (resid 5:17 or resid 19:20 or resid...I19 - 20
931(chain I and (resid 5:17 or resid 19:20 or resid...I22 - 24
941(chain I and (resid 5:17 or resid 19:20 or resid...I33 - 55
951(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 31
961(chain I and (resid 5:17 or resid 19:20 or resid...I58 - 59
971(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 67
981(chain I and (resid 5:17 or resid 19:20 or resid...I69 - 70
991(chain I and (resid 5:17 or resid 19:20 or resid...I0
9101(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9111(chain I and (resid 5:17 or resid 19:20 or resid...I77 - 86
9121(chain I and (resid 5:17 or resid 19:20 or resid...I96 - 97
9131(chain I and (resid 5:17 or resid 19:20 or resid...I99
9141(chain I and (resid 5:17 or resid 19:20 or resid...I129 - 159
9151(chain I and (resid 5:17 or resid 19:20 or resid...I167 - 183
9161(chain I and (resid 5:17 or resid 19:20 or resid...I185 - 2
9171(chain I and (resid 5:17 or resid 19:20 or resid...I2330
9181(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9191(chain I and (resid 5:17 or resid 19:20 or resid...I282 - 287
9201(chain I and (resid 5:17 or resid 19:20 or resid...I293
9211(chain I and (resid 5:17 or resid 19:20 or resid...I298
9221(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9231(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9241(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9251(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9261(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9271(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9281(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9291(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9301(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9311(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9321(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
1011(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 17
1021(chain J and (resid 5:17 or resid 19:20 or resid...J19 - 20
1031(chain J and (resid 5:17 or resid 19:20 or resid...J22 - 24
1041(chain J and (resid 5:17 or resid 19:20 or resid...J33 - 55
1051(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 31
1061(chain J and (resid 5:17 or resid 19:20 or resid...J58 - 59
1071(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 67
1081(chain J and (resid 5:17 or resid 19:20 or resid...J69 - 70
1091(chain J and (resid 5:17 or resid 19:20 or resid...J0
10101(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10111(chain J and (resid 5:17 or resid 19:20 or resid...J77 - 86
10121(chain J and (resid 5:17 or resid 19:20 or resid...J96 - 97
10131(chain J and (resid 5:17 or resid 19:20 or resid...J99
10141(chain J and (resid 5:17 or resid 19:20 or resid...J129 - 159
10151(chain J and (resid 5:17 or resid 19:20 or resid...J167 - 183
10161(chain J and (resid 5:17 or resid 19:20 or resid...J185 - 2
10171(chain J and (resid 5:17 or resid 19:20 or resid...J2330
10181(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10191(chain J and (resid 5:17 or resid 19:20 or resid...J282 - 287
10201(chain J and (resid 5:17 or resid 19:20 or resid...J293
10211(chain J and (resid 5:17 or resid 19:20 or resid...J298
10221(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10231(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10241(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10251(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10261(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10271(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10281(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10291(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10301(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10311(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10321(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
1111(chain K and (resid 5:17 or resid 19:20 or resid...K5 - 17
1121(chain K and (resid 5:17 or resid 19:20 or resid...K19 - 20
1131(chain K and (resid 5:17 or resid 19:20 or resid...K22 - 24
1141(chain K and (resid 5:17 or resid 19:20 or resid...K33 - 55
1151(chain K and (resid 5:17 or resid 19:20 or resid...K3 - 31
1161(chain K and (resid 5:17 or resid 19:20 or resid...K58 - 59
1171(chain K and (resid 5:17 or resid 19:20 or resid...K3 - 67
1181(chain K and (resid 5:17 or resid 19:20 or resid...K69 - 70
1191(chain K and (resid 5:17 or resid 19:20 or resid...K0
11101(chain K and (resid 5:17 or resid 19:20 or resid...K3 - 298
11111(chain K and (resid 5:17 or resid 19:20 or resid...K77 - 86
11121(chain K and (resid 5:17 or resid 19:20 or resid...K96 - 97
11131(chain K and (resid 5:17 or resid 19:20 or resid...K99
11141(chain K and (resid 5:17 or resid 19:20 or resid...K129 - 159
11151(chain K and (resid 5:17 or resid 19:20 or resid...K167 - 183
11161(chain K and (resid 5:17 or resid 19:20 or resid...K185 - 2
11171(chain K and (resid 5:17 or resid 19:20 or resid...K2330
11181(chain K and (resid 5:17 or resid 19:20 or resid...K3 - 298
11191(chain K and (resid 5:17 or resid 19:20 or resid...K282 - 287
11201(chain K and (resid 5:17 or resid 19:20 or resid...K293
11211(chain K and (resid 5:17 or resid 19:20 or resid...K295 - 2
1211(chain L and (resid 5:17 or resid 19:20 or resid...L5 - 17
1221(chain L and (resid 5:17 or resid 19:20 or resid...L19 - 20
1231(chain L and (resid 5:17 or resid 19:20 or resid...L22 - 24
1241(chain L and (resid 5:17 or resid 19:20 or resid...L33 - 55
1251(chain L and (resid 5:17 or resid 19:20 or resid...L3 - 31
1261(chain L and (resid 5:17 or resid 19:20 or resid...L58 - 59
1271(chain L and (resid 5:17 or resid 19:20 or resid...L3 - 67
1281(chain L and (resid 5:17 or resid 19:20 or resid...L69 - 70
1291(chain L and (resid 5:17 or resid 19:20 or resid...L0
12101(chain L and (resid 5:17 or resid 19:20 or resid...L3 - 298
12111(chain L and (resid 5:17 or resid 19:20 or resid...L77 - 86
12121(chain L and (resid 5:17 or resid 19:20 or resid...L96 - 97
12131(chain L and (resid 5:17 or resid 19:20 or resid...L99
12141(chain L and (resid 5:17 or resid 19:20 or resid...L129 - 159
12151(chain L and (resid 5:17 or resid 19:20 or resid...L167 - 183
12161(chain L and (resid 5:17 or resid 19:20 or resid...L185 - 2
12171(chain L and (resid 5:17 or resid 19:20 or resid...L2330
12181(chain L and (resid 5:17 or resid 19:20 or resid...L3 - 298
12191(chain L and (resid 5:17 or resid 19:20 or resid...L282 - 287
12201(chain L and (resid 5:17 or resid 19:20 or resid...L293
12211(chain L and (resid 5:17 or resid 19:20 or resid...L295 - 2

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要素

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タンパク質 , 1種, 12分子 ABCDEFGHIJKL

#1: タンパク質
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


分子量: 34176.293 Da / 分子数: 12 / 変異: H59K / 由来タイプ: 組換発現
由来: (組換発現) Campylobacter jejuni (カンピロバクター)
遺伝子: dapA / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A2U0QMK8, 4-hydroxy-tetrahydrodipicolinate synthase

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非ポリマー , 7種, 1672分子

#2: 化合物
ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C6H14O4 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 19 / 由来タイプ: 合成 / 式: C2H3O2 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 56 / 由来タイプ: 合成 / 式: C2H6O2 / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C4H10O3 / タイプ: SUBJECT OF INVESTIGATION
#7: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C3H8O3 / タイプ: SUBJECT OF INVESTIGATION
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1572 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.19 Å3/Da / 溶媒含有率: 43.95 %
結晶化温度: 288.15 K / 手法: マイクロバッチ法 / pH: 7.4
詳細: 0.3 M Magnesium acetate, 10 % PEG8000, 0.1 M Sodium acetate (pH 7.4)

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: CLSI / ビームライン: 08ID-1 / 波長: 0.97949 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2017年10月17日
放射モノクロメーター: Double Crystal Monochromator / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97949 Å / 相対比: 1
反射解像度: 2.1→38.583 Å / Num. obs: 204501 / % possible obs: 99.6 % / 冗長度: 15 % / Biso Wilson estimate: 25.94 Å2 / CC1/2: 0.9 / Net I/σ(I): 6.79
反射 シェル解像度: 2.1→2.175 Å / Rmerge(I) obs: 0.686 / Num. unique obs: 20464 / % possible all: 99.87

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
PHENIXdev_2398精密化
PDB_EXTRACT3.25データ抽出
HKL-3000データ削減
AMPLE位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4LY8

4ly8


解像度: 2.1→38.583 Å / SU ML: 0.27 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 25.14 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2526 10224 5 %
Rwork0.2056 194244 -
obs0.208 204468 99.69 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 67.73 Å2 / Biso mean: 27.9909 Å2 / Biso min: 11.97 Å2
精密化ステップサイクル: final / 解像度: 2.1→38.583 Å
タンパク質核酸リガンド溶媒全体
原子数27298 0 466 1572 29336
Biso mean--36.93 30.55 -
残基数----3547
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00228144
X-RAY DIFFRACTIONf_angle_d0.61337846
X-RAY DIFFRACTIONf_chiral_restr0.0444353
X-RAY DIFFRACTIONf_plane_restr0.0044824
X-RAY DIFFRACTIONf_dihedral_angle_d14.18417155
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A14103X-RAY DIFFRACTION5.655TORSIONAL
12B14103X-RAY DIFFRACTION5.655TORSIONAL
13C14103X-RAY DIFFRACTION5.655TORSIONAL
14D14103X-RAY DIFFRACTION5.655TORSIONAL
15E14103X-RAY DIFFRACTION5.655TORSIONAL
16F14103X-RAY DIFFRACTION5.655TORSIONAL
17G14103X-RAY DIFFRACTION5.655TORSIONAL
18H14103X-RAY DIFFRACTION5.655TORSIONAL
19I14103X-RAY DIFFRACTION5.655TORSIONAL
110J14103X-RAY DIFFRACTION5.655TORSIONAL
111K14103X-RAY DIFFRACTION5.655TORSIONAL
112L14103X-RAY DIFFRACTION5.655TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12390.31153410.26496494100
2.1239-2.14890.32993380.25836417100
2.1489-2.17510.31383440.25926530100
2.1751-2.20260.28383390.25086438100
2.2026-2.23160.30843410.27146490100
2.2316-2.26210.36893380.3075641899
2.2621-2.29450.31223400.25326459100
2.2945-2.32870.27493400.23856453100
2.3287-2.36510.29973440.23646531100
2.3651-2.40380.28323380.23466435100
2.4038-2.44530.30743410.23396463100
2.4453-2.48970.27053400.2326470100
2.4897-2.53760.28333440.22756534100
2.5376-2.58940.2833420.2166488100
2.5894-2.64570.28313390.22176445100
2.6457-2.70720.28693410.22486485100
2.7072-2.77490.26713410.21576477100
2.7749-2.84990.27573420.21776491100
2.8499-2.93380.2783400.21736474100
2.9338-3.02840.26353420.20796487100
3.0284-3.13660.25193410.20326484100
3.1366-3.26210.25793410.2126486100
3.2621-3.41050.25043410.2026477100
3.4105-3.59020.23743410.1984646799
3.5902-3.81490.24143400.1883645899
3.8149-4.10920.21293400.1769646999
4.1092-4.52220.20873390.1642643999
4.5222-5.17520.20573430.16436520100
5.1752-6.51510.21463420.18816484100
6.5151-9.390.18843410.1653648198

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万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

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

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る