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- PDB-7o74: Structure of cyanase from Pseudomonas lactis -

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基本情報

登録情報
データベース: PDB / ID: 7o74
タイトルStructure of cyanase from Pseudomonas lactis
要素Cyanate hydratase
キーワードLYASE / Hydrolase / Decamer / Nitrogen metabolism / Cyanate decomposition
機能・相同性
機能・相同性情報


cyanate metabolic process / cyanase / cyanate hydratase activity / DNA binding
類似検索 - 分子機能
Cyanate lyase, C-terminal / Cyanate hydratase / Cyanate lyase, C-terminal domain superfamily / Cyanate lyase C-terminal domain / Cyanate lyase C-terminal domain, Cyanate hydratase / Lambda repressor-like, DNA-binding domain superfamily
類似検索 - ドメイン・相同性
生物種Pseudomonas lactis (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.61 Å
データ登録者Brag, S. / Driller, J.H. / Pedersen, B.P.
引用ジャーナル: To Be Published
タイトル: Structure determination and analysis of unintentionally crystallized cyanase from Pseudomonas lactis
著者: Brag, S. / Driller, J.H. / Pedersen, B.P.
履歴
登録2021年4月12日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年4月21日Provider: repository / タイプ: Initial release
改定 1.12024年1月31日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Cyanate hydratase
B: Cyanate hydratase
C: Cyanate hydratase
D: Cyanate hydratase
E: Cyanate hydratase
F: Cyanate hydratase
G: Cyanate hydratase
H: Cyanate hydratase
I: Cyanate hydratase
J: Cyanate hydratase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)169,70419
ポリマ－169,38510
非ポリマー3199
水33,6341867
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area63830 Å2
ΔGint-510 kcal/mol
Surface area47380 Å2
手法PISA
単位格子
Length a, b, c (Å)130.146, 117.592, 106.991
Angle α, β, γ (deg.)90.000, 94.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11A-342-

HOH

21A-402-

HOH

31A-507-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 1 through 16 or resid 18...
21(chain B and (resid 1 through 16 or resid 18...
31(chain C and (resid 1 through 16 or resid 18...
41(chain D and (resid 1 through 16 or resid 18...
51(chain E and (resid 1 through 16 or resid 18...
61(chain F and (resid 1 through 16 or resid 18...
71(chain G and (resid 1 through 16 or resid 18...
81(chain H and (resid 1 through 16 or resid 18...
91(chain I and (resid 1 through 16 or resid 18...
101(chain J and (resid 1 through 16 or resid 18...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 16 or resid 18...A1 - 16
121(chain A and (resid 1 through 16 or resid 18...A18 - 38
131(chain A and (resid 1 through 16 or resid 18...A40 - 55
141(chain A and (resid 1 through 16 or resid 18...A57 - 60
151(chain A and (resid 1 through 16 or resid 18...A70 - 74
161(chain A and (resid 1 through 16 or resid 18...A1 - 156
171(chain A and (resid 1 through 16 or resid 18...A87 - 85
181(chain A and (resid 1 through 16 or resid 18...A0
191(chain A and (resid 1 through 16 or resid 18...A1 - 156
1101(chain A and (resid 1 through 16 or resid 18...A32 - 13336
1111(chain A and (resid 1 through 16 or resid 18...A1 - 156
1121(chain A and (resid 1 through 16 or resid 18...A139
1131(chain A and (resid 1 through 16 or resid 18...A139
1141(chain A and (resid 1 through 16 or resid 18...A141 - 153
1151(chain A and (resid 1 through 16 or resid 18...A155 - 156
211(chain B and (resid 1 through 16 or resid 18...B1 - 16
221(chain B and (resid 1 through 16 or resid 18...B18 - 38
231(chain B and (resid 1 through 16 or resid 18...B40 - 55
241(chain B and (resid 1 through 16 or resid 18...B70 - 74
251(chain B and (resid 1 through 16 or resid 18...B1 - 68
261(chain B and (resid 1 through 16 or resid 18...B76
271(chain B and (resid 1 through 16 or resid 18...B78
281(chain B and (resid 1 through 16 or resid 18...B87 - 129
291(chain B and (resid 1 through 16 or resid 18...B13
2101(chain B and (resid 1 through 16 or resid 18...B135 - 136
2111(chain B and (resid 1 through 16 or resid 18...B139
2121(chain B and (resid 1 through 16 or resid 18...B141 - 153
2131(chain B and (resid 1 through 16 or resid 18...B155 - 156
311(chain C and (resid 1 through 16 or resid 18...C1 - 16
321(chain C and (resid 1 through 16 or resid 18...C18 - 38
331(chain C and (resid 1 through 16 or resid 18...C1 - 156
341(chain C and (resid 1 through 16 or resid 18...C0
351(chain C and (resid 1 through 16 or resid 18...C62 - 68
361(chain C and (resid 1 through 16 or resid 18...C70 - 74
371(chain C and (resid 1 through 16 or resid 18...C76
381(chain C and (resid 1 through 16 or resid 18...C78 - 85
391(chain C and (resid 1 through 16 or resid 18...C87 - 129
3101(chain C and (resid 1 through 16 or resid 18...C132 - 133
3111(chain C and (resid 1 through 16 or resid 18...C135 - 136
3121(chain C and (resid 1 through 16 or resid 18...C139
3131(chain C and (resid 1 through 16 or resid 18...C141 - 153
3141(chain C and (resid 1 through 16 or resid 18...C155 - 156
411(chain D and (resid 1 through 16 or resid 18...D1 - 16
421(chain D and (resid 1 through 16 or resid 18...D18 - 38
431(chain D and (resid 1 through 16 or resid 18...D40 - 55
441(chain D and (resid 1 through 16 or resid 18...D57 - 60
451(chain D and (resid 1 through 16 or resid 18...D62 - 68
461(chain D and (resid 1 through 16 or resid 18...D70 - 74
471(chain D and (resid 1 through 16 or resid 18...D76
481(chain D and (resid 1 through 16 or resid 18...D78 - 85
491(chain D and (resid 1 through 16 or resid 18...D87 - 129
4101(chain D and (resid 1 through 16 or resid 18...D132 - 133
4111(chain D and (resid 1 through 16 or resid 18...D135 - 136
4121(chain D and (resid 1 through 16 or resid 18...D139
4131(chain D and (resid 1 through 16 or resid 18...D141 - 153
4141(chain D and (resid 1 through 16 or resid 18...D155 - 156
511(chain E and (resid 1 through 16 or resid 18...E1 - 16
521(chain E and (resid 1 through 16 or resid 18...E18 - 38
531(chain E and (resid 1 through 16 or resid 18...E40 - 55
541(chain E and (resid 1 through 16 or resid 18...E57 - 60
551(chain E and (resid 1 through 16 or resid 18...E62 - 68
561(chain E and (resid 1 through 16 or resid 18...E70 - 74
571(chain E and (resid 1 through 16 or resid 18...E76
581(chain E and (resid 1 through 16 or resid 18...E78 - 85
591(chain E and (resid 1 through 16 or resid 18...E87 - 129
5101(chain E and (resid 1 through 16 or resid 18...E132 - 133
5111(chain E and (resid 1 through 16 or resid 18...E135 - 136
5121(chain E and (resid 1 through 16 or resid 18...E139
5131(chain E and (resid 1 through 16 or resid 18...E141 - 153
5141(chain E and (resid 1 through 16 or resid 18...E155 - 156
611(chain F and (resid 1 through 16 or resid 18...F1 - 16
621(chain F and (resid 1 through 16 or resid 18...F18 - 38
631(chain F and (resid 1 through 16 or resid 18...F40 - 55
641(chain F and (resid 1 through 16 or resid 18...F57 - 60
651(chain F and (resid 1 through 16 or resid 18...F62 - 68
661(chain F and (resid 1 through 16 or resid 18...F70 - 74
671(chain F and (resid 1 through 16 or resid 18...F76
681(chain F and (resid 1 through 16 or resid 18...F78 - 85
691(chain F and (resid 1 through 16 or resid 18...F87 - 129
6101(chain F and (resid 1 through 16 or resid 18...F132 - 133
6111(chain F and (resid 1 through 16 or resid 18...F135 - 136
6121(chain F and (resid 1 through 16 or resid 18...F139
6131(chain F and (resid 1 through 16 or resid 18...F141 - 153
6141(chain F and (resid 1 through 16 or resid 18...F155 - 156
711(chain G and (resid 1 through 16 or resid 18...G1 - 16
721(chain G and (resid 1 through 16 or resid 18...G18 - 38
731(chain G and (resid 1 through 16 or resid 18...G40 - 55
741(chain G and (resid 1 through 16 or resid 18...G62 - 68
751(chain G and (resid 1 through 16 or resid 18...G70 - 74
761(chain G and (resid 1 through 16 or resid 18...G76
771(chain G and (resid 1 through 16 or resid 18...G78 - 85
781(chain G and (resid 1 through 16 or resid 18...G87 - 129
791(chain G and (resid 1 through 16 or resid 18...G132 - 133
7101(chain G and (resid 1 through 16 or resid 18...G135 - 136
7111(chain G and (resid 1 through 16 or resid 18...G139
7121(chain G and (resid 1 through 16 or resid 18...G141 - 153
7131(chain G and (resid 1 through 16 or resid 18...G155 - 156
811(chain H and (resid 1 through 16 or resid 18...H1 - 16
821(chain H and (resid 1 through 16 or resid 18...H18 - 38
831(chain H and (resid 1 through 16 or resid 18...H40 - 55
841(chain H and (resid 1 through 16 or resid 18...H57 - 60
851(chain H and (resid 1 through 16 or resid 18...H62 - 68
861(chain H and (resid 1 through 16 or resid 18...H70 - 74
871(chain H and (resid 1 through 16 or resid 18...H76
881(chain H and (resid 1 through 16 or resid 18...H78 - 85
891(chain H and (resid 1 through 16 or resid 18...H87 - 129
8101(chain H and (resid 1 through 16 or resid 18...H132 - 133
8111(chain H and (resid 1 through 16 or resid 18...H135 - 136
8121(chain H and (resid 1 through 16 or resid 18...H139
8131(chain H and (resid 1 through 16 or resid 18...H141 - 153
8141(chain H and (resid 1 through 16 or resid 18...H155 - 156
911(chain I and (resid 1 through 16 or resid 18...I1 - 16
921(chain I and (resid 1 through 16 or resid 18...I18 - 38
931(chain I and (resid 1 through 16 or resid 18...I40 - 55
941(chain I and (resid 1 through 16 or resid 18...I57 - 60
951(chain I and (resid 1 through 16 or resid 18...I62 - 68
961(chain I and (resid 1 through 16 or resid 18...I70 - 74
971(chain I and (resid 1 through 16 or resid 18...I76
981(chain I and (resid 1 through 16 or resid 18...I78 - 85
991(chain I and (resid 1 through 16 or resid 18...I87 - 129
9101(chain I and (resid 1 through 16 or resid 18...I132 - 133
9111(chain I and (resid 1 through 16 or resid 18...I135 - 136
9121(chain I and (resid 1 through 16 or resid 18...I139
9131(chain I and (resid 1 through 16 or resid 18...I141 - 153
9141(chain I and (resid 1 through 16 or resid 18...I155 - 156
1011(chain J and (resid 1 through 16 or resid 18...J1 - 16
1021(chain J and (resid 1 through 16 or resid 18...J18 - 38
1031(chain J and (resid 1 through 16 or resid 18...J40 - 55
1041(chain J and (resid 1 through 16 or resid 18...J57 - 60
1051(chain J and (resid 1 through 16 or resid 18...J62 - 68
1061(chain J and (resid 1 through 16 or resid 18...J70 - 74
1071(chain J and (resid 1 through 16 or resid 18...J76
1081(chain J and (resid 1 through 16 or resid 18...J78 - 85
1091(chain J and (resid 1 through 16 or resid 18...J87 - 129
10101(chain J and (resid 1 through 16 or resid 18...J132 - 133
10111(chain J and (resid 1 through 16 or resid 18...J135 - 136
10121(chain J and (resid 1 through 16 or resid 18...J139
10131(chain J and (resid 1 through 16 or resid 18...J141 - 153
10141(chain J and (resid 1 through 16 or resid 18...J155 - 156

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要素

#1: タンパク質
Cyanate hydratase / Cyanase / Cyanate hydrolase / Cyanate lyase


分子量: 16938.469 Da / 分子数: 10 / 由来タイプ: 天然 / 由来: (天然) Pseudomonas lactis (バクテリア) / 参照: UniProt: A0A218ZZ45, cyanase
#2: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 9 / 由来タイプ: 合成 / 式: Cl
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1867 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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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: 2.32 Å3/Da / 溶媒含有率: 47 %
結晶化温度: 292.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: MemGold B9 0.1M Potassium chloride 0.02M Tris7.0 20% w/v PEG 4000

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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: Diamond / ビームライン: I24 / 波長: 0.9686 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2020年2月2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: 0.9686 Å / 相対比: 1
反射解像度: 1.61→43.57 Å / Num. obs: 202687 / % possible obs: 97.4 % / 冗長度: 6.944 % / Biso Wilson estimate: 20.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.169 / Rrim(I) all: 0.183 / Χ2: 0.812 / Net I/σ(I): 8.28 / Num. measured all: 1407503 / Scaling rejects: 81
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.61-1.656.7072.7061.049697415348144590.2412.93194.2
1.65-1.696.9842.1581.4110055014968143980.3432.33196.2
1.69-1.746.9251.8841.669711614534140230.4242.03696.5
1.74-1.86.8031.5482.099314614170136910.531.67796.6
1.8-1.867.0161.2422.779284913662132340.6961.34196.9
1.86-1.926.8670.9683.518850713283128880.7841.04897
1.92-1.997.0490.7344.528774312801124470.8710.79197.2
1.99-2.077.150.555.88569212294119850.9280.59397.5
2.07-2.177.1160.4177.058223411824115560.9560.4597.7
2.17-2.277.1190.3128.547863211299110460.9710.33797.8
2.27-2.47.1510.2519.857555210760105650.9790.2798.2
2.4-2.547.0990.19611.327105910187100100.9860.21298.3
2.54-2.727.0070.16412.665933955194090.9880.17898.5
2.72-2.937.0490.12515.0362030892088000.9920.13698.7
2.93-3.216.9250.117.4456184820681130.9940.10898.9
3.21-3.596.8760.07920.850487741773420.9950.08599
3.59-4.156.6680.06823.0343535658165290.9950.07499.2
4.15-5.086.4030.06223.8735398557155280.9960.06799.2
5.08-7.196.5470.06123.7528029431542810.9960.06699.2
7.19-43.576.6530.05526.115853240623830.9970.0699

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation7.22 Å46.54 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19精密化
XDSFeb 5, 2021データ削減
XSCALEFeb 5, 2021データスケーリング
PHASER2.8.3位相決定
PDB_EXTRACT3.27データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 4y42

4y42


解像度: 1.61→43.57 Å / SU ML: 0.2 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 21.31 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1898 2022 1 %
Rwork0.1639 200388 -
obs0.1641 202410 97.23 %
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: 84.11 Å2 / Biso mean: 25.1156 Å2 / Biso min: 10.84 Å2
精密化ステップサイクル: final / 解像度: 1.61→43.57 Å
タンパク質核酸リガンド溶媒全体
原子数11920 0 9 1867 13796
Biso mean--23.37 34.34 -
残基数----1560
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3880X-RAY DIFFRACTION1.145TORSIONAL
12B3880X-RAY DIFFRACTION1.145TORSIONAL
13C3880X-RAY DIFFRACTION1.145TORSIONAL
14D3880X-RAY DIFFRACTION1.145TORSIONAL
15E3880X-RAY DIFFRACTION1.145TORSIONAL
16F3880X-RAY DIFFRACTION1.145TORSIONAL
17G3880X-RAY DIFFRACTION1.145TORSIONAL
18H3880X-RAY DIFFRACTION1.145TORSIONAL
19I3880X-RAY DIFFRACTION1.145TORSIONAL
110J3880X-RAY DIFFRACTION1.145TORSIONAL
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 (%)
1.61-1.650.32441370.3135134241356192
1.65-1.690.30221400.2875141351427596
1.69-1.740.34371430.2684141181426196
1.74-1.80.27851430.2616142101435397
1.8-1.860.26881440.2285142471439197
1.86-1.940.23221430.1897142311437497
1.94-2.020.21631460.1742143051445197
2.02-2.130.1891440.1643143541449898
2.13-2.260.18571450.1557143951454098
2.26-2.440.19111490.1521144571460698
2.44-2.680.20191440.1577144691461398
2.68-3.070.18991470.1581145491469699
3.07-3.870.16471490.1396146591480899
3.87-43.570.13271480.1312148351498399

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