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- PDB-6di8: Crystal structure of bovine alpha-chymotrypsin in space group P65 -

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基本情報

登録情報
データベース: PDB / ID: 6di8
タイトルCrystal structure of bovine alpha-chymotrypsin in space group P65
要素
  • Chymotrypsin A chain A
  • Chymotrypsin A chain B
  • Chymotrypsin A chain C
キーワードHYDROLASE / Trypsin-like serine protease / endopeptidase
機能・相同性
機能・相同性情報


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region
類似検索 - 分子機能
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
類似検索 - ドメイン・相同性
Chymotrypsinogen A
類似検索 - 構成要素
生物種Bos taurus (ウシ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.859 Å
データ登録者Marshall, A.C. / Keiller, B.G. / Bruning, J.B.
引用ジャーナル: Crystals / 年: 2018
タイトル: Crystal Structure of Bovine Alpha-Chymotrypsin in Space Group P65
著者: Marshall, A.C. / Keiller, B.G. / Pederick, J.L. / Abell, A.D. / Bruning, J.B.
履歴
登録2018年5月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年1月23日Provider: repository / タイプ: Initial release
改定 1.12023年10月11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
改定 1.22024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Chymotrypsin A chain A
B: Chymotrypsin A chain B
C: Chymotrypsin A chain C
D: Chymotrypsin A chain A
E: Chymotrypsin A chain B
F: Chymotrypsin A chain C
G: Chymotrypsin A chain A
H: Chymotrypsin A chain B
I: Chymotrypsin A chain C
J: Chymotrypsin A chain A
K: Chymotrypsin A chain B
L: Chymotrypsin A chain C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)102,29925
ポリマ－101,05012
非ポリマー1,24913
水19,8171100
1
A: Chymotrypsin A chain A
B: Chymotrypsin A chain B
C: Chymotrypsin A chain C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,7438
ポリマ－25,2633
非ポリマー4805
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-97 kcal/mol
Surface area10210 Å2
手法PISA
2
D: Chymotrypsin A chain A
E: Chymotrypsin A chain B
F: Chymotrypsin A chain C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,4555
ポリマ－25,2633
非ポリマー1922
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-81 kcal/mol
Surface area10380 Å2
手法PISA
3
G: Chymotrypsin A chain A
H: Chymotrypsin A chain B
I: Chymotrypsin A chain C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,4555
ポリマ－25,2633
非ポリマー1922
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-87 kcal/mol
Surface area10050 Å2
手法PISA
4
J: Chymotrypsin A chain A
K: Chymotrypsin A chain B
L: Chymotrypsin A chain C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,6477
ポリマ－25,2633
非ポリマー3844
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-101 kcal/mol
Surface area10570 Å2
手法PISA
単位格子
Length a, b, c (Å)126.810, 126.810, 122.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21(chain D and (resid 1 through 10 or (resid 11...
31(chain G and (resid 1 through 10 or (resid 11...
41(chain J and (resid 1 through 10 or (resid 11...
12(chain B and (resid 16 through 17 or resid 19...
22(chain E and (resid 16 through 17 or resid 19...
32(chain H and (resid 16 through 17 or resid 19...
42(chain K and (resid 16 through 17 or resid 19...
13(chain C and (resid 149 through 152 or resid 154...
23(chain F and (resid 149 through 152 or resid 154...
33(chain I and (resid 149 through 152 or resid 154...
43(chain L and (resid 149 through 152 or resid 154...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 13
211(chain D and (resid 1 through 10 or (resid 11...D1 - 10
221(chain D and (resid 1 through 10 or (resid 11...D11
231(chain D and (resid 1 through 10 or (resid 11...D1 - 13
241(chain D and (resid 1 through 10 or (resid 11...D1 - 13
251(chain D and (resid 1 through 10 or (resid 11...D1 - 13
261(chain D and (resid 1 through 10 or (resid 11...D1 - 13
311(chain G and (resid 1 through 10 or (resid 11...G1 - 10
321(chain G and (resid 1 through 10 or (resid 11...G11
331(chain G and (resid 1 through 10 or (resid 11...G1 - 13
341(chain G and (resid 1 through 10 or (resid 11...G1 - 13
351(chain G and (resid 1 through 10 or (resid 11...G1 - 13
411(chain J and (resid 1 through 10 or (resid 11...J1 - 10
421(chain J and (resid 1 through 10 or (resid 11...J11
431(chain J and (resid 1 through 10 or (resid 11...J1 - 13
112(chain B and (resid 16 through 17 or resid 19...B16 - 17
122(chain B and (resid 16 through 17 or resid 19...B19 - 48
132(chain B and (resid 16 through 17 or resid 19...B50 - 62
142(chain B and (resid 16 through 17 or resid 19...B64
152(chain B and (resid 16 through 17 or resid 19...B0
162(chain B and (resid 16 through 17 or resid 19...B72 - 75
172(chain B and (resid 16 through 17 or resid 19...B79 - 89
182(chain B and (resid 16 through 17 or resid 19...B0
192(chain B and (resid 16 through 17 or resid 19...B16 - 146
1102(chain B and (resid 16 through 17 or resid 19...B16 - 146
1112(chain B and (resid 16 through 17 or resid 19...B16 - 146
212(chain E and (resid 16 through 17 or resid 19...E16 - 17
222(chain E and (resid 16 through 17 or resid 19...E19 - 35
232(chain E and (resid 16 through 17 or resid 19...E36
242(chain E and (resid 16 through 17 or resid 19...E16 - 146
252(chain E and (resid 16 through 17 or resid 19...E16 - 146
262(chain E and (resid 16 through 17 or resid 19...E16 - 146
272(chain E and (resid 16 through 17 or resid 19...E16 - 146
312(chain H and (resid 16 through 17 or resid 19...H16 - 17
322(chain H and (resid 16 through 17 or resid 19...H19 - 48
332(chain H and (resid 16 through 17 or resid 19...H50 - 62
342(chain H and (resid 16 through 17 or resid 19...H64
352(chain H and (resid 16 through 17 or resid 19...H77 - 8
362(chain H and (resid 16 through 17 or resid 19...H77 - 90
372(chain H and (resid 16 through 17 or resid 19...H16 - 146
382(chain H and (resid 16 through 17 or resid 19...H16 - 146
392(chain H and (resid 16 through 17 or resid 19...H16 - 146
3102(chain H and (resid 16 through 17 or resid 19...H16 - 146
3112(chain H and (resid 16 through 17 or resid 19...H16 - 146
3122(chain H and (resid 16 through 17 or resid 19...H16 - 146
3132(chain H and (resid 16 through 17 or resid 19...H16 - 146
412(chain K and (resid 16 through 17 or resid 19...K16 - 17
422(chain K and (resid 16 through 17 or resid 19...K19 - 35
432(chain K and (resid 16 through 17 or resid 19...K36
442(chain K and (resid 16 through 17 or resid 19...K16 - 146
452(chain K and (resid 16 through 17 or resid 19...K16 - 146
462(chain K and (resid 16 through 17 or resid 19...K16 - 146
113(chain C and (resid 149 through 152 or resid 154...C149 - 152
123(chain C and (resid 149 through 152 or resid 154...C154 - 166
133(chain C and (resid 149 through 152 or resid 154...C168 - 174
143(chain C and (resid 149 through 152 or resid 154...C149 - 245
153(chain C and (resid 149 through 152 or resid 154...C149 - 245
163(chain C and (resid 149 through 152 or resid 154...C149 - 245
173(chain C and (resid 149 through 152 or resid 154...C149 - 245
183(chain C and (resid 149 through 152 or resid 154...C149 - 245
193(chain C and (resid 149 through 152 or resid 154...C149 - 245
1103(chain C and (resid 149 through 152 or resid 154...C149 - 245
213(chain F and (resid 149 through 152 or resid 154...F149 - 152
223(chain F and (resid 149 through 152 or resid 154...F154 - 166
233(chain F and (resid 149 through 152 or resid 154...F168 - 174
243(chain F and (resid 149 through 152 or resid 154...F175
253(chain F and (resid 149 through 152 or resid 154...F149 - 245
263(chain F and (resid 149 through 152 or resid 154...F149 - 245
273(chain F and (resid 149 through 152 or resid 154...F149 - 245
283(chain F and (resid 149 through 152 or resid 154...F149 - 245
293(chain F and (resid 149 through 152 or resid 154...F149 - 245
2103(chain F and (resid 149 through 152 or resid 154...F149 - 245
313(chain I and (resid 149 through 152 or resid 154...I149 - 152
323(chain I and (resid 149 through 152 or resid 154...I154 - 166
333(chain I and (resid 149 through 152 or resid 154...I168 - 174
343(chain I and (resid 149 through 152 or resid 154...I175
353(chain I and (resid 149 through 152 or resid 154...I149 - 245
363(chain I and (resid 149 through 152 or resid 154...I149 - 245
373(chain I and (resid 149 through 152 or resid 154...I149 - 245
383(chain I and (resid 149 through 152 or resid 154...I149 - 245
393(chain I and (resid 149 through 152 or resid 154...I149 - 245
3103(chain I and (resid 149 through 152 or resid 154...I149 - 245
413(chain L and (resid 149 through 152 or resid 154...L149 - 152
423(chain L and (resid 149 through 152 or resid 154...L154 - 166
433(chain L and (resid 149 through 152 or resid 154...L168 - 191
443(chain L and (resid 149 through 152 or resid 154...L193 - 245

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質・ペプチド
Chymotrypsin A chain A


分子量: 1253.511 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 器官: Pancreas / 参照: UniProt: P00766, chymotrypsin
#2: タンパク質
Chymotrypsin A chain B


分子量: 13934.556 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 器官: Pancreas / 参照: UniProt: P00766, chymotrypsin
#3: タンパク質
Chymotrypsin A chain C


分子量: 10074.495 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 器官: Pancreas / 参照: UniProt: P00766, chymotrypsin
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 13 / 由来タイプ: 合成 / 式: SO4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1100 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY

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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: 2.76 Å3/Da / 溶媒含有率: 55.38 %
結晶化温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: Protein (lyophilized powder, Worthington, code: CDTLCK) was dissolved in 0.1 M HEPES (pH 7.0) to a final concentration of 20mg/mL. Crystallisation condition was 2 M ammonium sulphate, with ...詳細: Protein (lyophilized powder, Worthington, code: CDTLCK) was dissolved in 0.1 M HEPES (pH 7.0) to a final concentration of 20mg/mL. Crystallisation condition was 2 M ammonium sulphate, with equal volume (1 uL) of protein and reservoir solution in the drop

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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: Australian Synchrotron / ビームライン: MX1 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2015年2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: 0.9537 Å / 相対比: 1
反射解像度: 1.86→29.55 Å / Num. obs: 93385 / % possible obs: 100 % / 冗長度: 9.3 % / Biso Wilson estimate: 25.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.041 / Rrim(I) all: 0.126 / Net I/σ(I): 12.2 / Num. measured all: 868057 / Scaling rejects: 1475
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.86-1.896.81.9243130846060.3830.7792.083199.7
10.18-29.559.50.04255235790.9990.0140.04529.396.3

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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
Rotation3.67 Å29.55 Å
Translation3.67 Å29.55 Å

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解析

ソフトウェア
名称バージョン分類NB
PHENIX(dev_3084)精密化
MOSFLMデータ削減
Aimless0.5.17データスケーリング
PHASER2.8.2位相決定
PDB_EXTRACT3.24データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 4Q2K

4q2k


解像度: 1.859→28.132 Å / SU ML: 0.26 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 25.46 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2252 4889 5.25 %
Rwork0.1885 88296 -
obs0.1904 93185 99.81 %
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: 119.53 Å2 / Biso mean: 34.8988 Å2 / Biso min: 5.08 Å2
精密化ステップサイクル: final / 解像度: 1.859→28.132 Å
タンパク質核酸リガンド溶媒全体
原子数7049 0 65 1100 8214
Biso mean--82.63 44.01 -
残基数----964
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A209X-RAY DIFFRACTION5.355TORSIONAL
12D209X-RAY DIFFRACTION5.355TORSIONAL
13G209X-RAY DIFFRACTION5.355TORSIONAL
14J209X-RAY DIFFRACTION5.355TORSIONAL
21B2082X-RAY DIFFRACTION5.355TORSIONAL
22E2082X-RAY DIFFRACTION5.355TORSIONAL
23H2082X-RAY DIFFRACTION5.355TORSIONAL
24K2082X-RAY DIFFRACTION5.355TORSIONAL
31C1659X-RAY DIFFRACTION5.355TORSIONAL
32F1659X-RAY DIFFRACTION5.355TORSIONAL
33I1659X-RAY DIFFRACTION5.355TORSIONAL
34L1659X-RAY DIFFRACTION5.355TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.859-1.88010.35411620.33662900306299
1.8801-1.90230.33871390.32782951309099
1.9023-1.92550.33421670.331129363103100
1.9255-1.94980.36241700.310129563126100
1.9498-1.97550.36331740.288229163090100
1.9755-2.00250.32821780.27729183096100
2.0025-2.03110.32761710.263129003071100
2.0311-2.06140.31161770.247329333110100
2.0614-2.09360.28651600.251529593119100
2.0936-2.1280.28271340.24329633097100
2.128-2.16460.25161180.239530013119100
2.1646-2.2040.23421720.23129293101100
2.204-2.24640.26371860.227229063092100
2.2464-2.29220.2621600.217529503110100
2.2922-2.3420.22631950.201329353130100
2.342-2.39650.2641590.201229383097100
2.3965-2.45640.27331510.200129273078100
2.4564-2.52270.23091640.197129533117100
2.5227-2.59690.26391740.183229353109100
2.5969-2.68070.21371430.184229403083100
2.6807-2.77640.25831790.187629513130100
2.7764-2.88750.23481460.196429863132100
2.8875-3.01870.23511760.196829163092100
3.0187-3.17770.21681430.17729753118100
3.1777-3.37650.19211710.170129393110100
3.3765-3.63670.18671740.14729473121100
3.6367-4.00170.1761490.134429893138100
4.0017-4.57860.14941600.12229573117100
4.5786-5.76040.16831590.144929843143100
5.7604-28.1350.2081780.18672906308497
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0793-0.73820.70093.9764-3.44787.27150.107-0.27480.31770.48070.1968-0.38560.18310.8093-0.21520.32440.0809-0.03910.2483-0.09390.2056-57.9569-3.56116.9562
23.5427-1.49550.35423.84960.821.8956-0.0131-0.1732-0.14770.01580.0772-0.16050.24990.0582-0.05210.22040.0364-0.00430.14120.01780.1469-53.2852-15.3899-0.2665
33.86451.2427-0.57841.8490.75974.12650.0930.38320.0375-0.4946-0.0443-0.0825-0.003-0.0751-0.04350.32470.0656-0.00060.17050.00760.1542-53.4071-17.2526-11.98
48.93998.9901-3.8692.0119-1.28545.71490.3551-0.4949-1.53760.5466-0.0732-0.83130.57-0.7144-0.29770.40830.0047-0.1160.41960.05840.4128-62.3928-19.83034.071
56.07521.17730.62321.905-0.48121.87160.01250.6192-0.3793-0.6881-0.1185-0.68960.22220.33020.10540.47630.13280.18240.27020.01460.3855-45.9927-14.6202-15.4248
61.5016-0.3088-0.10142.8089-0.61561.7904-0.02140.12810.0433-0.1346-0.0215-0.4009-0.07310.12280.03240.22910.03090.01580.1214-0.01750.1966-51.8851-8.4341-3.1528
71.9985-8.15558.81988.6113-3.75566.762-0.0951-1.7837-0.5823-0.04010.8531.1798-0.5613-0.5934-0.69690.41370.1659-0.10780.32960.02750.4418-48.9871-23.18749.264
83.25860.4619-0.08015.943-2.05962.7216-0.1678-0.65230.44850.1036-0.0928-0.5589-0.09150.32170.2250.24650.0617-0.08910.1911-0.08840.2837-46.0684-7.26055.8171
94.4154-0.8368-1.82362.3589-0.5683.0083-0.0513-0.20950.51960.0492-0.1967-1.5338-0.05911.31760.27010.30980.02210.01910.4550.10730.9127-31.4035-4.5871-4.0381
102.73690.37691.5934.8378-0.4444.4343-0.0712-0.06960.1945-0.03870.0279-0.47260.00620.18590.04150.1840.03330.02520.1629-0.02230.2403-45.8003-7.284-0.5712
111.9738-0.92071.24814.1873-2.43214.01930.07320.12050.10490.0061-0.1992-0.94580.23540.52040.1430.21740.06150.00660.2204-0.01550.4361-37.7799-8.9228-1.4026
125.47910.40812.32028.45510.49656.2784-0.28090.3042-0.2086-1.15490.2733-0.57460.4506-0.30.00540.59480.02240.06780.24140.0230.2268-51.5501-4.5947-20.2999
131.869-0.9453-2.06860.64390.22976.4788-0.1285-0.029-0.39630.1456-0.12410.2954-0.0359-0.27780.30670.26050.013-0.0390.1525-0.0040.4728-69.16955.35647.9602
141.7392-0.19440.52721.8539-1.34952.3839-0.10680.00970.02210.02150.1061-0.1723-0.3304-0.01010.00770.28170.0199-0.00290.1155-0.04050.281-73.90917.6485-4.5107
159.77767.19433.51739.4323-0.12687.37050.151-0.68780.61961.1813-0.54470.2639-1.28010.11820.40980.5946-0.0403-0.02910.3004-0.02660.4291-64.435521.50373.9774
167.2661.45471.12182.50470.28212.9608-0.05980.21290.0529-0.62970.05660.3345-0.3539-0.20770.00850.39710.0575-0.05760.1377-0.03530.2565-80.898216.26-15.2859
171.193-0.05480.25222.9478-0.0361.583-0.01870.0208-0.28580.00750.1065-0.04830.0391-0.0435-0.09020.22320.0267-0.01350.1163-0.0230.3532-74.62359.559-3.9156
181.99841.9975-8.30899.9095.55282.00710.3345-0.30570.73010.34490.5748-1.06270.42590.0806-0.93090.5920.13060.00650.29860.02440.4296-78.275824.71669.3868
192.1167-0.3460.04083.0585-0.33351.9729-0.0146-0.1785-0.2560.4087-0.01610.1950.1854-0.10860.01280.26820.06370.08960.1590.03750.3794-80.79678.55035.7363
202.9938-0.21133.4269.41490.29866.15480.2977-0.3204-1.410.4467-0.29181.5830.0692-0.98150.00190.31890.00510.03950.4015-0.02231.106-98.02645.3018-2.1313
211.77950.1819-0.59623.4224-0.13843.8743-0.01-0.0416-0.53910.1391-0.02790.4045-0.0364-0.30180.03060.2150.04150.00180.15860.03430.4523-84.49898.077-1.1879
221.11830.0968-0.96331.8562-0.30123.52490.03170.1937-0.3319-0.1231-0.06520.3586-0.0446-0.33460.04840.22440.012-0.05530.1464-0.0350.4076-82.88528.1677-7.7496
236.61114.6759-0.3758.85912.9393.2783-0.18760.5630.6074-0.27330.21380.64350.2048-0.52730.02560.2128-0.0519-0.01190.22580.07480.2357-69.585-3.258513.2664
247.01234.2888-0.75414.3816-0.33560.0649-0.4520.86450.1419-0.41830.41580.3165-0.17490.0204-0.01420.2553-0.0551-0.04090.210.06260.1867-73.7038-10.556612.7156
254.32411.0014-1.02586.9759-3.87995.11140.00050.1287-0.66890.01210.00610.41880.6097-0.2099-0.0240.3643-0.0643-0.04020.2375-0.03220.3337-73.1481-23.30224.9804
265.82371.3458-0.15274.7362-0.5833.70750.1747-0.2865-0.06170.2137-0.06260.20040.195-0.2456-0.11030.3107-0.0534-0.00050.15680.01620.1018-73.639-14.64326.7646
273.9379-1.22580.31822.15780.09673.82360.1725-0.4939-0.02790.6062-0.04120.1511-0.16970.1233-0.09640.3467-0.06920.01110.1916-0.0040.144-73.5189-16.883331.7019
289.2216-8.9534-5.09472.01311.81396.39190.22070.6178-1.3724-0.9665-0.29951.06770.23260.33390.00330.4040.0015-0.10920.3991-0.06370.4019-64.3776-19.833115.6177
292.0584-3.2108-4.55373.53461.61819.1959-0.0528-0.2833-0.59070.5394-0.04590.37580.20890.30250.02070.4288-0.0928-0.00710.2950.00480.1885-70.3274-17.999934.8941
305.52610.0652-0.90112.36370.00852.63560.0793-0.7403-0.11010.853-0.15810.61170.3114-0.25210.08780.4771-0.11960.19490.2798-0.0430.3344-80.3349-12.955434.928
312.0997-0.4875-0.18013.62170.31751.5887-0.0032-0.23680.25310.09970.00120.3224-0.2859-0.05380.02020.3388-0.0473-0.00410.1758-0.02360.224-73.2156-0.868325.0324
325.63251.10140.34636.4340.94730.5812-0.0903-0.0686-0.5432-0.54220.17810.388-0.0012-0.2534-0.08040.2459-0.0536-0.06120.19460.05450.213-80.6573-13.286814.4779
334.00353.39850.31814.73870.76041.98020.03650.24990.0591-0.23820.01690.0432-0.0136-0.1557-0.0510.2298-0.0588-0.07490.22270.05840.1819-79.8524-12.044512.9936
345.43230.8373-4.39935.6420.31076.89830.23010.69221.203-0.20490.15881.342-0.0931-1.267-0.40670.3005-0.0461-0.01080.5803-0.06361.0622-98.0632-4.764322.0193
354.692.45541.78454.6774-3.32317.8008-0.2066-0.27590.20440.289-0.29281.2874-0.2439-1.17110.5050.2694-0.01340.08120.2865-0.10260.6605-91.4624-4.394726.2523
363.3444-1.04261.48374.6729-0.12554.756-0.01570.00590.1970.11080.00630.49450.0535-0.16140.00030.1813-0.02910.03910.15910.01580.2311-80.9648-7.09120.3064
372.1555-0.45951.48357.00410.16594.79540.067-0.01820.48710.4396-0.53830.791-0.2428-0.10870.43850.3219-0.0827-0.14450.3062-0.0130.7078-92.6886-14.222414.1461
383.89670.77132.25074.36761.31634.4142-0.0704-0.37540.38320.8756-0.24320.50810.3041-0.27550.34970.403-0.06330.14480.191-0.0440.2936-80.1513-4.616934.0237
391.49730.6569-1.97570.88930.26324.9204-0.01430.0773-0.3889-0.39270.0954-0.0610.25590.1793-0.05340.28-0.0048-0.01180.1643-0.05690.4524-57.61865.358611.7021
402.49280.074-0.4172.85160.86281.8429-0.05810.2162-0.3085-0.39590.09250.214-0.13480.0284-0.0650.2545-0.0439-0.03120.1505-0.01780.3288-52.970712.04312.7086
416.16011.55821.3857.7153.4085.6172-0.27-0.00770.9918-0.63140.1140.408-0.91050.19740.16770.3089-0.0461-0.0010.19230.03470.3531-52.936625.229325.0944
427.17451.8247-0.09122.84191.07523.6274-0.390.3778-0.2698-0.16840.32910.0702-0.2224-0.0795-0.01040.2959-0.0069-0.05140.11520.01710.2754-52.835316.26726.706
433.3321-0.24620.86780.3410.56872.53970.0603-0.2145-0.04780.3096-0.00220.3095-0.1871-0.0808-0.03840.3353-0.01020.02140.14180.04040.3-53.381418.234831.6083
442.0004-8.415-1.15559.29432.85152.0210.3280.52140.7071-0.7696-0.51170.1198-1.9182-0.3310.1360.5169-0.0013-0.08020.33910.040.4129-62.060921.171515.5098
452.0474-2.36786.68015.5717-0.03026.0702-0.0753-0.02980.11210.42450.10770.1477-0.5612-0.1129-0.07170.3960.00850.08610.27910.09590.3226-56.222120.094534.7791
462.01661.5119-2.01212.73122.16534.7842-0.1413-0.4878-0.00360.7826-0.2245-0.9602-0.35860.51120.24050.3778-0.0422-0.18240.24370.07270.4815-37.750213.270335.2589
471.99882.10281.74224.26310.51253.9305-0.1612-0.37530.21540.4866-0.10270.5553-0.3264-0.40040.22780.33420.02360.04480.17150.02860.3683-58.926516.297334.3325
480.63730.3826-0.35553.758-0.41351.70140.0199-0.1513-0.58240.06940.1363-0.09750.21080.0246-0.15120.2807-0.0337-0.04690.12450.02350.4647-53.68522.46725.1724
493.93640.62340.76594.2824-0.72212.3555-0.03370.14690.0813-0.4891-0.001-0.2298-0.16140.25150.04020.2851-0.06260.02880.1725-0.060.2842-45.876614.609214.4912
503.4771.8151-0.76335.3341-0.76023.7266-0.190.52150.1918-0.23220.3345-0.4684-0.4549-0.0405-0.12130.3515-0.07020.0030.178-0.03110.3082-51.004319.756410.9435
511.94942.12541.67412.88751.98272.69-0.08070.4539-1.0336-0.31410.3423-1.45330.04030.9962-0.16660.313-0.00460.05720.3918-0.02490.8678-32.17914.430620.2251
522.1802-0.11020.00242.89571.03333.5090.01440.0117-0.5293-0.1598-0.0519-0.33780.01170.21350.01860.2253-0.0370.01360.1504-0.03330.4562-42.34958.08820.9668
531.1464-0.1362-0.77931.54170.12422.83950.0879-0.1693-0.28850.1111-0.0172-0.2445-0.07280.2523-0.06530.2304-0.0177-0.04710.13880.02990.3792-43.92058.167827.4651
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )A1 - 13
2X-RAY DIFFRACTION2chain 'B' and (resid 16 through 48 )B16 - 48
3X-RAY DIFFRACTION3chain 'B' and (resid 49 through 68 )B49 - 68
4X-RAY DIFFRACTION4chain 'B' and (resid 69 through 80 )B69 - 80
5X-RAY DIFFRACTION5chain 'B' and (resid 81 through 103 )B81 - 103
6X-RAY DIFFRACTION6chain 'B' and (resid 104 through 146 )B104 - 146
7X-RAY DIFFRACTION7chain 'C' and (resid 149 through 153 )C149 - 153
8X-RAY DIFFRACTION8chain 'C' and (resid 154 through 164 )C154 - 164
9X-RAY DIFFRACTION9chain 'C' and (resid 165 through 184 )C165 - 184
10X-RAY DIFFRACTION10chain 'C' and (resid 185 through 215 )C185 - 215
11X-RAY DIFFRACTION11chain 'C' and (resid 216 through 234 )C216 - 234
12X-RAY DIFFRACTION12chain 'C' and (resid 235 through 245 )C235 - 245
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 13 )D1 - 13
14X-RAY DIFFRACTION14chain 'E' and (resid 16 through 68 )E16 - 68
15X-RAY DIFFRACTION15chain 'E' and (resid 69 through 80 )E69 - 80
16X-RAY DIFFRACTION16chain 'E' and (resid 81 through 103 )E81 - 103
17X-RAY DIFFRACTION17chain 'E' and (resid 104 through 146 )E104 - 146
18X-RAY DIFFRACTION18chain 'F' and (resid 149 through 153 )F149 - 153
19X-RAY DIFFRACTION19chain 'F' and (resid 154 through 164 )F154 - 164
20X-RAY DIFFRACTION20chain 'F' and (resid 165 through 175 )F165 - 175
21X-RAY DIFFRACTION21chain 'F' and (resid 176 through 205 )F176 - 205
22X-RAY DIFFRACTION22chain 'F' and (resid 206 through 245 )F206 - 245
23X-RAY DIFFRACTION23chain 'G' and (resid 1 through 13 )G1 - 13
24X-RAY DIFFRACTION24chain 'H' and (resid 16 through 29 )H16 - 29
25X-RAY DIFFRACTION25chain 'H' and (resid 30 through 39 )H30 - 39
26X-RAY DIFFRACTION26chain 'H' and (resid 40 through 48 )H40 - 48
27X-RAY DIFFRACTION27chain 'H' and (resid 49 through 68 )H49 - 68
28X-RAY DIFFRACTION28chain 'H' and (resid 69 through 80 )H69 - 80
29X-RAY DIFFRACTION29chain 'H' and (resid 81 through 90 )H81 - 90
30X-RAY DIFFRACTION30chain 'H' and (resid 91 through 113 )H91 - 113
31X-RAY DIFFRACTION31chain 'H' and (resid 114 through 133 )H114 - 133
32X-RAY DIFFRACTION32chain 'H' and (resid 134 through 146 )H134 - 146
33X-RAY DIFFRACTION33chain 'I' and (resid 149 through 164 )I149 - 164
34X-RAY DIFFRACTION34chain 'I' and (resid 165 through 175 )I165 - 175
35X-RAY DIFFRACTION35chain 'I' and (resid 176 through 184 )I176 - 184
36X-RAY DIFFRACTION36chain 'I' and (resid 185 through 215 )I185 - 215
37X-RAY DIFFRACTION37chain 'I' and (resid 216 through 224 )I216 - 224
38X-RAY DIFFRACTION38chain 'I' and (resid 225 through 245 )I225 - 245
39X-RAY DIFFRACTION39chain 'J' and (resid 1 through 13 )J1 - 13
40X-RAY DIFFRACTION40chain 'K' and (resid 16 through 29 )K16 - 29
41X-RAY DIFFRACTION41chain 'K' and (resid 30 through 39 )K30 - 39
42X-RAY DIFFRACTION42chain 'K' and (resid 40 through 48 )K40 - 48
43X-RAY DIFFRACTION43chain 'K' and (resid 49 through 68 )K49 - 68
44X-RAY DIFFRACTION44chain 'K' and (resid 69 through 80 )K69 - 80
45X-RAY DIFFRACTION45chain 'K' and (resid 81 through 90 )K81 - 90
46X-RAY DIFFRACTION46chain 'K' and (resid 91 through 103 )K91 - 103
47X-RAY DIFFRACTION47chain 'K' and (resid 104 through 113 )K104 - 113
48X-RAY DIFFRACTION48chain 'K' and (resid 114 through 133 )K114 - 133
49X-RAY DIFFRACTION49chain 'K' and (resid 134 through 146 )K134 - 146
50X-RAY DIFFRACTION50chain 'L' and (resid 149 through 158 )L149 - 158
51X-RAY DIFFRACTION51chain 'L' and (resid 159 through 175 )L159 - 175
52X-RAY DIFFRACTION52chain 'L' and (resid 176 through 205 )L176 - 205
53X-RAY DIFFRACTION53chain 'L' and (resid 206 through 245 )L206 - 245

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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

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

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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