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- PDB-5zli: Crystal structure of glutamine synthetase from helicobacter pylori -

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基本情報

登録情報
データベース: PDB / ID: 5zli
タイトルCrystal structure of glutamine synthetase from helicobacter pylori
要素Glutamine synthetase
キーワードLIGASE / glutamine synthetase / enzyme / GS / helicobacter pylori / STRUCTURAL PROTEIN
機能・相同性
機能・相同性情報


nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / metal ion binding / membrane / cytoplasm
類似検索 - 分子機能
Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain ...Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Glutamine synthetase
類似検索 - 構成要素
生物種Helicobacter pylori (ピロリ菌)
手法X線回折 / シンクロトロン / 解像度: 2.8 Å
データ登録者Joo, H.K. / Lee, J.Y.
資金援助 韓国, 2件
組織認可番号国
National Research Foundation (Korea)2017R1D1A1B03032109 韓国
710013-03-1-SB120 韓国
引用ジャーナル: Sci Rep / 年: 2018
タイトル: Structural Analysis of Glutamine Synthetase from Helicobacter pylori.
著者: Joo, H.K. / Park, Y.W. / Jang, Y.Y. / Lee, J.Y.
履歴
登録2018年3月28日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02018年8月29日Provider: repository / タイプ: Initial release
改定 1.12024年3月27日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase


分子量 (理論値)分子数
合計 (水以外)327,4776
ポリマ－327,4776
非ポリマー00
水00
1
A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase

A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase


分子量 (理論値)分子数
合計 (水以外)654,95512
ポリマ－654,95512
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_958-x+4,y,-z+31
単位格子
Length a, b, c (Å)191.085, 131.462, 131.411
Angle α, β, γ (deg.)90.000, 122.670, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 10 or resseq 12 or resseq...
21(chain B and (resseq 10 or resseq 12 or resseq...
31(chain C and (resseq 10 or resseq 12 or resseq...
41(chain D and (resseq 10 or resseq 12 or resseq...
51(chain E and (resseq 10 or resseq 12 or resseq...
61(chain F and (resseq 10 or resseq 12 or resseq...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 10 or resseq 12 or resseq...A10
121(chain A and (resseq 10 or resseq 12 or resseq...A12
131(chain A and (resseq 10 or resseq 12 or resseq...A15 - 16
141(chain A and (resseq 10 or resseq 12 or resseq...A0
151(chain A and (resseq 10 or resseq 12 or resseq...A8 - 481
161(chain A and (resseq 10 or resseq 12 or resseq...A8 - 481
171(chain A and (resseq 10 or resseq 12 or resseq...A127 - 1
181(chain A and (resseq 10 or resseq 12 or resseq...A177 - 17
191(chain A and (resseq 10 or resseq 12 or resseq...A8 - 481
1101(chain A and (resseq 10 or resseq 12 or resseq...A181 - 185
1111(chain A and (resseq 10 or resseq 12 or resseq...A187 - 207
1121(chain A and (resseq 10 or resseq 12 or resseq...A209 - 211
1131(chain A and (resseq 10 or resseq 12 or resseq...A219 - 233
1141(chain A and (resseq 10 or resseq 12 or resseq...A235 - 287
1151(chain A and (resseq 10 or resseq 12 or resseq...A303 - 3
1161(chain A and (resseq 10 or resseq 12 or resseq...A8 - 481
1171(chain A and (resseq 10 or resseq 12 or resseq...A366 - 399
1181(chain A and (resseq 10 or resseq 12 or resseq...A411 - 41
1191(chain A and (resseq 10 or resseq 12 or resseq...A421 - 427
1201(chain A and (resseq 10 or resseq 12 or resseq...A421 - 427
1211(chain A and (resseq 10 or resseq 12 or resseq...A429 - 443
1221(chain A and (resseq 10 or resseq 12 or resseq...A445 - 448
1231(chain A and (resseq 10 or resseq 12 or resseq...A450 - 481
211(chain B and (resseq 10 or resseq 12 or resseq...B10
221(chain B and (resseq 10 or resseq 12 or resseq...B12
231(chain B and (resseq 10 or resseq 12 or resseq...B15 - 16
241(chain B and (resseq 10 or resseq 12 or resseq...B18 - 53
251(chain B and (resseq 10 or resseq 12 or resseq...B0
261(chain B and (resseq 10 or resseq 12 or resseq...B7 - 481
271(chain B and (resseq 10 or resseq 12 or resseq...B165 - 166
281(chain B and (resseq 10 or resseq 12 or resseq...B177 - 179
291(chain B and (resseq 10 or resseq 12 or resseq...B7 - 481
2101(chain B and (resseq 10 or resseq 12 or resseq...B187 - 207
2111(chain B and (resseq 10 or resseq 12 or resseq...B209 - 211
2121(chain B and (resseq 10 or resseq 12 or resseq...B217
2131(chain B and (resseq 10 or resseq 12 or resseq...B2119 - 2
2141(chain B and (resseq 10 or resseq 12 or resseq...B290 - 301
2151(chain B and (resseq 10 or resseq 12 or resseq...B303 - 360
2161(chain B and (resseq 10 or resseq 12 or resseq...B303 - 360
2171(chain B and (resseq 10 or resseq 12 or resseq...B401 - 409
2181(chain B and (resseq 10 or resseq 12 or resseq...B411 - 419
2191(chain B and (resseq 10 or resseq 12 or resseq...B421 - 424
2201(chain B and (resseq 10 or resseq 12 or resseq...B416 - 417
2211(chain B and (resseq 10 or resseq 12 or resseq...B429 - 447
2221(chain B and (resseq 10 or resseq 12 or resseq...B445 - 443
2231(chain B and (resseq 10 or resseq 12 or resseq...B445 - 448
2241(chain B and (resseq 10 or resseq 12 or resseq...B450 - 481
311(chain C and (resseq 10 or resseq 12 or resseq...C10
321(chain C and (resseq 10 or resseq 12 or resseq...C12
331(chain C and (resseq 10 or resseq 12 or resseq...C15 - 16
341(chain C and (resseq 10 or resseq 12 or resseq...C184 - 125
351(chain C and (resseq 10 or resseq 12 or resseq...C124 - 12163
361(chain C and (resseq 10 or resseq 12 or resseq...C165 - 166
371(chain C and (resseq 10 or resseq 12 or resseq...C168 - 174
381(chain C and (resseq 10 or resseq 12 or resseq...C177 - 179
391(chain C and (resseq 10 or resseq 12 or resseq...C181 - 185
3101(chain C and (resseq 10 or resseq 12 or resseq...C187 - 207
3111(chain C and (resseq 10 or resseq 12 or resseq...C209 - 21
3121(chain C and (resseq 10 or resseq 12 or resseq...C217
3131(chain C and (resseq 10 or resseq 12 or resseq...C219 - 233
3141(chain C and (resseq 10 or resseq 12 or resseq...C235 - 287
3151(chain C and (resseq 10 or resseq 12 or resseq...C303 - 360
3161(chain C and (resseq 10 or resseq 12 or resseq...C362 - 36
3171(chain C and (resseq 10 or resseq 12 or resseq...C366 - 399
3181(chain C and (resseq 10 or resseq 12 or resseq...C401 - 409
3191(chain C and (resseq 10 or resseq 12 or resseq...C411 - 414
3201(chain C and (resseq 10 or resseq 12 or resseq...C416 - 417
3211(chain C and (resseq 10 or resseq 12 or resseq...C421 - 427
3221(chain C and (resseq 10 or resseq 12 or resseq...C429 - 443
3231(chain C and (resseq 10 or resseq 12 or resseq...C445 - 448
3241(chain C and (resseq 10 or resseq 12 or resseq...C450 - 481
411(chain D and (resseq 10 or resseq 12 or resseq...D10
421(chain D and (resseq 10 or resseq 12 or resseq...D12
431(chain D and (resseq 10 or resseq 12 or resseq...D15 - 16
441(chain D and (resseq 10 or resseq 12 or resseq...D184 - 125
451(chain D and (resseq 10 or resseq 12 or resseq...D124 - 12163
461(chain D and (resseq 10 or resseq 12 or resseq...D165 - 166
471(chain D and (resseq 10 or resseq 12 or resseq...D168 - 174
481(chain D and (resseq 10 or resseq 12 or resseq...D177 - 179
491(chain D and (resseq 10 or resseq 12 or resseq...D181 - 185
4101(chain D and (resseq 10 or resseq 12 or resseq...D187 - 207
4111(chain D and (resseq 10 or resseq 12 or resseq...D209 - 21
4121(chain D and (resseq 10 or resseq 12 or resseq...D217
4131(chain D and (resseq 10 or resseq 12 or resseq...D219 - 233
4141(chain D and (resseq 10 or resseq 12 or resseq...D235 - 287
4151(chain D and (resseq 10 or resseq 12 or resseq...D303 - 360
4161(chain D and (resseq 10 or resseq 12 or resseq...D362 - 36
4171(chain D and (resseq 10 or resseq 12 or resseq...D366 - 399
4181(chain D and (resseq 10 or resseq 12 or resseq...D401 - 409
4191(chain D and (resseq 10 or resseq 12 or resseq...D411 - 414
4201(chain D and (resseq 10 or resseq 12 or resseq...D416 - 417
4211(chain D and (resseq 10 or resseq 12 or resseq...D421 - 427
4221(chain D and (resseq 10 or resseq 12 or resseq...D429 - 443
4231(chain D and (resseq 10 or resseq 12 or resseq...D445 - 448
4241(chain D and (resseq 10 or resseq 12 or resseq...D450 - 481
511(chain E and (resseq 10 or resseq 12 or resseq...E10
521(chain E and (resseq 10 or resseq 12 or resseq...E12
531(chain E and (resseq 10 or resseq 12 or resseq...E15 - 16
541(chain E and (resseq 10 or resseq 12 or resseq...E18 - 53
551(chain E and (resseq 10 or resseq 12 or resseq...E0
561(chain E and (resseq 10 or resseq 12 or resseq...E8 - 481
571(chain E and (resseq 10 or resseq 12 or resseq...E165 - 166
581(chain E and (resseq 10 or resseq 12 or resseq...E177 - 179
591(chain E and (resseq 10 or resseq 12 or resseq...E8 - 481
5101(chain E and (resseq 10 or resseq 12 or resseq...E187 - 207
5111(chain E and (resseq 10 or resseq 12 or resseq...E209 - 211
5121(chain E and (resseq 10 or resseq 12 or resseq...E217
5131(chain E and (resseq 10 or resseq 12 or resseq...E2119 - 2
5141(chain E and (resseq 10 or resseq 12 or resseq...E290 - 301
5151(chain E and (resseq 10 or resseq 12 or resseq...E303 - 360
5161(chain E and (resseq 10 or resseq 12 or resseq...E303 - 360
5171(chain E and (resseq 10 or resseq 12 or resseq...E401 - 409
5181(chain E and (resseq 10 or resseq 12 or resseq...E411 - 419
5191(chain E and (resseq 10 or resseq 12 or resseq...E421 - 424
5201(chain E and (resseq 10 or resseq 12 or resseq...E416 - 417
5211(chain E and (resseq 10 or resseq 12 or resseq...E429 - 447
5221(chain E and (resseq 10 or resseq 12 or resseq...E445 - 443
5231(chain E and (resseq 10 or resseq 12 or resseq...E445 - 448
5241(chain E and (resseq 10 or resseq 12 or resseq...E450 - 481
611(chain F and (resseq 10 or resseq 12 or resseq...F10
621(chain F and (resseq 10 or resseq 12 or resseq...F12
631(chain F and (resseq 10 or resseq 12 or resseq...F15 - 16
641(chain F and (resseq 10 or resseq 12 or resseq...F184 - 125
651(chain F and (resseq 10 or resseq 12 or resseq...F124 - 12163
661(chain F and (resseq 10 or resseq 12 or resseq...F165 - 166
671(chain F and (resseq 10 or resseq 12 or resseq...F168 - 174
681(chain F and (resseq 10 or resseq 12 or resseq...F177 - 179
691(chain F and (resseq 10 or resseq 12 or resseq...F181 - 185
6101(chain F and (resseq 10 or resseq 12 or resseq...F187 - 207
6111(chain F and (resseq 10 or resseq 12 or resseq...F209 - 21
6121(chain F and (resseq 10 or resseq 12 or resseq...F217
6131(chain F and (resseq 10 or resseq 12 or resseq...F219 - 233
6141(chain F and (resseq 10 or resseq 12 or resseq...F235 - 287
6151(chain F and (resseq 10 or resseq 12 or resseq...F303 - 360
6161(chain F and (resseq 10 or resseq 12 or resseq...F362 - 36
6171(chain F and (resseq 10 or resseq 12 or resseq...F366 - 399
6181(chain F and (resseq 10 or resseq 12 or resseq...F401 - 409
6191(chain F and (resseq 10 or resseq 12 or resseq...F411 - 414
6201(chain F and (resseq 10 or resseq 12 or resseq...F416 - 417
6211(chain F and (resseq 10 or resseq 12 or resseq...F421 - 427
6221(chain F and (resseq 10 or resseq 12 or resseq...F429 - 443
6231(chain F and (resseq 10 or resseq 12 or resseq...F445 - 448
6241(chain F and (resseq 10 or resseq 12 or resseq...F450 - 481

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要素

#1: タンパク質
Glutamine synthetase / GS / Glutamate--ammonia ligase / Glutamine synthetase I beta / GSI beta


分子量: 54579.543 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Helicobacter pylori (strain ATCC 700392 / 26695) (ピロリ菌)
株: ATCC 700392 / 26695 / 遺伝子: glnA, HP_0512 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P94845, glutamine synthetase

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.18 Å3/Da / 溶媒含有率: 43.52 %
結晶化温度: 296 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: PEG 6000, choline, Hepes

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: PAL/PLS / ビームライン: 5C (4A) / 波長: 0.9795 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2016年3月18日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9795 Å / 相対比: 1
反射解像度: 2.8→50 Å / Num. obs: 67460 / % possible obs: 99.5 % / 冗長度: 3.3 % / Biso Wilson estimate: 49.19 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.076 / Rrim(I) all: 0.14 / Χ2: 1.085 / Net I/σ(I): 7 / Num. measured all: 224008
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.853.40.43133640.7580.2760.5130.81299.8
2.85-2.93.40.38133430.80.2440.4530.88599.4
2.9-2.963.30.34933680.8170.2250.4160.92999.8
2.96-3.023.30.31433310.8580.2040.3750.92799.6
3.02-3.083.10.26833860.8750.1810.3251.11799.7
3.08-3.153.20.25833730.8940.1710.311.1399.8
3.15-3.233.40.2433900.9050.1540.2861.05299.6
3.23-3.323.50.21133400.9290.1330.251.13799.9
3.32-3.423.50.18733780.9450.1190.2221.19399.6
3.42-3.533.40.17233630.9470.110.2041.18999.7
3.53-3.653.40.1533780.9550.0960.1791.22399.5
3.65-3.83.30.12933450.9690.0840.1541.18399.5
3.8-3.973.20.11833800.9740.0780.1411.3599.2
3.97-4.1830.10133370.9760.070.1231.23799.3
4.18-4.443.40.09433860.9780.060.1121.12799.6
4.44-4.793.40.0933650.980.0580.1071.08899.3
4.79-5.273.40.08434200.9830.0550.1011.00499.6
5.27-6.033.10.08433800.9810.0560.1011.03699.8
6.03-7.593.40.07633990.9880.0480.0910.98299.6
7.59-503.30.06234340.9910.040.0741.13198.6

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
HKL-2000データ削減
HKL-2000データスケーリング
PDB_EXTRACT3.24データ抽出
PHASER位相決定
精密化解像度: 2.8→19.996 Å / SU ML: 0.39 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 24.61
Rfactor反射数%反射
Rfree0.2601 1982 2.97 %
Rwork0.1899 --
obs0.192 66840 99.57 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 107.6 Å2 / Biso mean: 43.9134 Å2 / Biso min: 14.38 Å2
精密化ステップサイクル: final / 解像度: 2.8→19.996 Å
タンパク質核酸リガンド溶媒全体
原子数22540 0 0 0 22540
残基数----2846
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01123140
X-RAY DIFFRACTIONf_angle_d1.27831283
X-RAY DIFFRACTIONf_chiral_restr0.0683260
X-RAY DIFFRACTIONf_plane_restr0.0094103
X-RAY DIFFRACTIONf_dihedral_angle_d18.11813665
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A12079X-RAY DIFFRACTION12.586TORSIONAL
12B12079X-RAY DIFFRACTION12.586TORSIONAL
13C12079X-RAY DIFFRACTION12.586TORSIONAL
14D12079X-RAY DIFFRACTION12.586TORSIONAL
15E12079X-RAY DIFFRACTION12.586TORSIONAL
16F12079X-RAY DIFFRACTION12.586TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.86990.32351400.205146014741100
2.8699-2.94730.32191420.208346224764100
2.9473-3.03370.26371410.21546104751100
3.0337-3.13130.32481430.21646684811100
3.1313-3.24270.31481390.218945474686100
3.2427-3.3720.29911420.214846734815100
3.372-3.52460.28811410.206446094750100
3.5246-3.70940.26881410.202346184759100
3.7094-3.94010.27061410.20194595473699
3.9401-4.24170.27571410.19634649479099
4.2417-4.66360.23561430.18446544797100
4.6636-5.32730.25161410.180546304771100
5.3273-6.67010.2591430.187446744817100
6.6701-19.99640.16941440.13544708485299

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万見について

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お知らせ

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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

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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

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