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- PDB-6dqy: Crystal Structure analysis of Superoxide Dismutase from Trichoder... -

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基本情報

登録情報
データベース: PDB / ID: 6dqy
タイトルCrystal Structure analysis of Superoxide Dismutase from Trichoderma reesei
要素Superoxide dismutase
キーワードOXIDOREDUCTASE / enzymatic activity
機能・相同性
機能・相同性情報


superoxide dismutase / superoxide dismutase activity / mitochondrion / metal ion binding
類似検索 - 分子機能
: / Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain ...: / Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
: / Superoxide dismutase
類似検索 - 構成要素
生物種Hypocrea jecorina (菌類)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.3 Å
データ登録者Mendoza, E.R. / Stelmastchuk, L.B.F. / Ferreira Junior, J.R.S. / Garratt, R.C.
資金援助 ブラジル, 1件
組織認可番号
Sao Paulo Research Foundation (FAPESP)2014/01855-2 ブラジル
引用ジャーナル: To Be Published
タイトル: Crystal Structure of Superoxide Dismutase from Trichoderma reesei
著者: Mendoza, E.R. / Stelmastchuk, L.B.F. / Ferreira Junior, J.R.S. / Garratt, R.C.
履歴
登録2018年6月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年12月12日Provider: repository / タイプ: Initial release
改定 1.12020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22024年3月13日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Superoxide dismutase
B: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
E: Superoxide dismutase
F: Superoxide dismutase
G: Superoxide dismutase
H: Superoxide dismutase
I: Superoxide dismutase
J: Superoxide dismutase
K: Superoxide dismutase
L: Superoxide dismutase
M: Superoxide dismutase
N: Superoxide dismutase
O: Superoxide dismutase
P: Superoxide dismutase
Q: Superoxide dismutase
R: Superoxide dismutase
S: Superoxide dismutase
T: Superoxide dismutase
U: Superoxide dismutase
V: Superoxide dismutase
W: Superoxide dismutase
X: Superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)559,56548
ポリマ-558,24724
非ポリマー1,31924
49,6672757
1
A: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
O: Superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,2618
ポリマ-93,0414
非ポリマー2204
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-53 kcal/mol
Surface area32320 Å2
手法PISA
2
B: Superoxide dismutase
G: Superoxide dismutase
I: Superoxide dismutase
T: Superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,2618
ポリマ-93,0414
非ポリマー2204
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-54 kcal/mol
Surface area32390 Å2
手法PISA
3
E: Superoxide dismutase
J: Superoxide dismutase
P: Superoxide dismutase
S: Superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,2618
ポリマ-93,0414
非ポリマー2204
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-49 kcal/mol
Surface area32480 Å2
手法PISA
4
F: Superoxide dismutase
K: Superoxide dismutase
M: Superoxide dismutase
Q: Superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,2618
ポリマ-93,0414
非ポリマー2204
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-56 kcal/mol
Surface area32450 Å2
手法PISA
5
H: Superoxide dismutase
U: Superoxide dismutase
V: Superoxide dismutase
W: Superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,2618
ポリマ-93,0414
非ポリマー2204
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-57 kcal/mol
Surface area32550 Å2
手法PISA
6
L: Superoxide dismutase
N: Superoxide dismutase
R: Superoxide dismutase
X: Superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,2618
ポリマ-93,0414
非ポリマー2204
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-53 kcal/mol
Surface area32430 Å2
手法PISA
単位格子
Length a, b, c (Å)73.770, 113.060, 162.710
Angle α, β, γ (deg.)91.590, 93.790, 89.980
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and resid 3 through 200)
21(chain B and resid 3 through 200)
31(chain C and resid 3 through 200)
41(chain D and resid 3 through 200)
51(chain E and resid 3 through 200)
61(chain F and resid 3 through 200)
71(chain G and resid 3 through 200)
81(chain H and resid 3 through 200)
91(chain I and resid 3 through 200)
101(chain J and resid 3 through 200)
111(chain K and resid 3 through 200)
121(chain L and resid 3 through 200)
131(chain M and resid 3 through 200)
141(chain N and resid 3 through 200)
151(chain O and resid 3 through 200)
161(chain P and resid 3 through 200)
171(chain Q and resid 3 through 200)
181(chain R and resid 3 through 200)
191(chain S and resid 3 through 200)
201(chain T and resid 3 through 200)
211(chain U and resid 3 through 200)
221(chain V and resid 3 through 200)
231(chain W and resid 3 through 200)
241(chain X and resid 3 through 200)

NCSドメイン領域:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 3 - 200 / Label seq-ID: 3 - 200

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 3 through 200)AA
2(chain B and resid 3 through 200)BB
3(chain C and resid 3 through 200)CC
4(chain D and resid 3 through 200)DD
5(chain E and resid 3 through 200)EE
6(chain F and resid 3 through 200)FF
7(chain G and resid 3 through 200)GG
8(chain H and resid 3 through 200)HH
9(chain I and resid 3 through 200)II
10(chain J and resid 3 through 200)JJ
11(chain K and resid 3 through 200)KK
12(chain L and resid 3 through 200)LL
13(chain M and resid 3 through 200)MM
14(chain N and resid 3 through 200)NN
15(chain O and resid 3 through 200)OO
16(chain P and resid 3 through 200)PP
17(chain Q and resid 3 through 200)QQ
18(chain R and resid 3 through 200)RR
19(chain S and resid 3 through 200)SS
20(chain T and resid 3 through 200)TT
21(chain U and resid 3 through 200)UU
22(chain V and resid 3 through 200)VV
23(chain W and resid 3 through 200)WW
24(chain X and resid 3 through 200)XX

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要素

#1: タンパク質 ...
Superoxide dismutase


分子量: 23260.285 Da / 分子数: 24 / 由来タイプ: 組換発現 / 由来: (組換発現) Hypocrea jecorina (菌類) / : QM6a / 遺伝子: TRIREDRAFT_66345 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: G0RQS7, superoxide dismutase
#2: 化合物...
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 24 / 由来タイプ: 合成 / : Mn
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2757 / 由来タイプ: 天然 / : H2O

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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: 2.44 Å3/Da / 溶媒含有率: 49.56 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 / 詳細: 100mM Bis-Tris pH 7.0, 25% PEG3350 / PH範囲: 6.5-7.0

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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: APS / ビームライン: 21-ID-G / 波長: 0.9786 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2016年2月11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: 0.9786 Å / 相対比: 1
反射解像度: 2.3→93.98 Å / Num. all: 226540 / Num. obs: 226540 / % possible obs: 97.2 % / 冗長度: 3.9 % / Biso Wilson estimate: 22.86 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.049 / Rrim(I) all: 0.098 / Rsym value: 0.084 / Net I/σ(I): 11.8 / Num. measured all: 875231
反射 シェル

Diffraction-ID: 1 / 冗長度: 3.8 %

解像度 (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.420.301123159326340.9040.0220.0420.0364.496.2
7.27-93.980.0362726972190.9970.0360.0720.0622297.8

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解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
SCALA3.3.22データスケーリング
PDB_EXTRACT3.24データ抽出
iMOSFLMデータ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.3→81.146 Å / SU ML: 0.24 / 交差検証法: THROUGHOUT / σ(F): 1.98 / 位相誤差: 20.47
Rfactor反射数%反射
Rfree0.2066 11460 5.06 %
Rwork0.1621 --
obs0.1643 226479 97.22 %
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: 113.4 Å2 / Biso mean: 31.2597 Å2 / Biso min: 6.14 Å2
精密化ステップサイクル: final / 解像度: 2.3→81.146 Å
タンパク質核酸リガンド溶媒全体
原子数38662 0 24 2757 41443
Biso mean--23.11 30.71 -
残基数----4983
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00739741
X-RAY DIFFRACTIONf_angle_d0.77754094
X-RAY DIFFRACTIONf_chiral_restr0.055823
X-RAY DIFFRACTIONf_plane_restr0.0066923
X-RAY DIFFRACTIONf_dihedral_angle_d10.90723111
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsタイプ
11A22422X-RAY DIFFRACTION4.87TORSIONAL
12B22422X-RAY DIFFRACTION4.87TORSIONAL
13C22422X-RAY DIFFRACTION4.87TORSIONAL
14D22422X-RAY DIFFRACTION4.87TORSIONAL
15E22422X-RAY DIFFRACTION4.87TORSIONAL
16F22422X-RAY DIFFRACTION4.87TORSIONAL
17G22422X-RAY DIFFRACTION4.87TORSIONAL
18H22422X-RAY DIFFRACTION4.87TORSIONAL
19I22422X-RAY DIFFRACTION4.87TORSIONAL
110J22422X-RAY DIFFRACTION4.87TORSIONAL
111K22422X-RAY DIFFRACTION4.87TORSIONAL
112L22422X-RAY DIFFRACTION4.87TORSIONAL
113M22422X-RAY DIFFRACTION4.87TORSIONAL
114N22422X-RAY DIFFRACTION4.87TORSIONAL
115O22422X-RAY DIFFRACTION4.87TORSIONAL
116P22422X-RAY DIFFRACTION4.87TORSIONAL
117Q22422X-RAY DIFFRACTION4.87TORSIONAL
118R22422X-RAY DIFFRACTION4.87TORSIONAL
119S22422X-RAY DIFFRACTION4.87TORSIONAL
120T22422X-RAY DIFFRACTION4.87TORSIONAL
121U22422X-RAY DIFFRACTION4.87TORSIONAL
122V22422X-RAY DIFFRACTION4.87TORSIONAL
123W22422X-RAY DIFFRACTION4.87TORSIONAL
124X22422X-RAY DIFFRACTION4.87TORSIONAL
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 (%)
2.3-2.32610.25953880.19117050743896
2.3261-2.35350.24363620.18987102746496
2.3535-2.38220.22123340.18547134746896
2.3822-2.41240.24393580.18187163752196
2.4124-2.44410.25083680.18367100746896
2.4441-2.47760.25963480.18417110745896
2.4776-2.5130.23453310.17077166749797
2.513-2.55050.23343610.17587201756297
2.5505-2.59040.23763650.17957128749397
2.5904-2.63280.23463770.17737191756897
2.6328-2.67820.23183750.1857108748397
2.6782-2.72690.26494300.18767151758197
2.7269-2.77940.24134120.19077042745497
2.7794-2.83610.23244350.18057230766597
2.8361-2.89780.23733910.18167104749597
2.8978-2.96520.2464040.18387194759897
2.9652-3.03940.24823970.18217129752697
3.0394-3.12150.21423820.1817170755297
3.1215-3.21340.21033920.17877277766998
3.2134-3.31710.22493840.18777161754598
3.3171-3.43570.22453920.17947169756198
3.4357-3.57320.21123630.16697208757198
3.5732-3.73590.20563810.16567238761998
3.7359-3.93280.17283800.14417223760398
3.9328-4.17920.15284490.13117148759798
4.1792-4.50190.16223680.12577247761598
4.5019-4.95490.15623550.12117278763398
4.9549-5.67170.17913940.13447239763398
5.6717-7.14510.19084450.14237143758898
7.1451-81.19620.15723390.13447215755497
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.3414-1.81810.36943.2272-0.57910.39320.06190.13920.2724-0.1672-0.0568-0.42830.00370.0999-0.01140.1341-0.0330.03780.1602-0.01360.196181.5366-51.0646203.6217
21.9337-1.94571.53723.1898-1.80491.880.08630.19190.0008-0.0784-0.1117-0.00050.04260.1144-0.00450.1313-0.00880.02620.143-0.02940.1846175.119-57.3993201.776
31.53840.6967-0.45161.3481-0.0562.34570.1360.4407-0.3167-0.1189-0.01020.23330.3761-0.55550.10780.317-0.0795-0.21070.4782-0.01940.373152.7483-58.011191.9119
43.43150.81862.33260.96740.89673.16260.16090.15840.0246-0.03520.28170.56780.0764-1.1571-0.2860.1601-0.04060.0150.34540.03860.4083154.1014-53.1386204.0696
54.2253-0.3823-0.03561.304-0.32267.09850.19310.07710.10220.0394-0.25680.27010.4878-0.18680.0670.1523-0.0247-0.00430.0773-0.00510.1949164.3557-59.0838205.2108
65.65560.71680.91411.58490.08755.96890.22210.306-0.4913-0.3214-0.18820.32931.233-0.5124-0.06560.2863-0.0329-0.06580.173-0.05340.3196161.1005-63.2715202.0126
71.5310.18181.77480.02720.25712.50940.18080.2405-0.35750.01710.0730.47990.6314-0.0173-0.1850.265-0.0433-0.04670.1986-0.04840.2314168.1219-60.301202.4403
81.562-0.56880.31231.3772-0.21172.316-0.0413-0.19740.0695-0.0412-0.07040.29-0.0222-0.10940.06230.1313-0.02080.02870.122-0.00460.172167.1739-44.7242212.9575
92.22690.0087-0.59851.6603-0.32386.24090.03410.0604-0.0424-0.04120.07360.51690.0384-0.53210.02650.1543-0.019-0.00430.1458-0.02050.2413160.2003-44.7306204.4728
103.90281.90332.11766.12420.92173.37950.10110.6924-0.1939-0.8701-0.10530.3610.1005-0.09510.06120.2198-0.0163-0.05980.2585-0.030.1858164.2597-54.0702189.9258
114.80963.6924.34253.16342.44276.997-0.19020.9065-1.051-1.09770.1001-0.47720.71560.60020.07870.54590.05370.01380.3844-0.00730.3976174.7328-62.139191.5487
123.6164-1.55460.38613.5995-0.08882.23940.03920.05490.1587-0.1810.0579-0.0618-0.2729-0.1655-0.09260.1946-0.01730.04270.11870.02330.1298158.1017-18.8393201.2117
131.0957-0.9401-1.00431.01820.62541.07890.17510.24940.0334-0.2134-0.2123-0.0013-0.1214-0.13910.0350.1507-0.0148-0.00190.12160.01790.1685150.281-14.1778208.3466
144.62872.1346-0.50452.726-0.86942.9180.2671-0.3070.1460.3898-0.3632-0.3345-0.3660.45390.10320.1112-0.0791-0.01910.2310.0120.2674173.513-16.1529225.1504
153.29471.0770.71791.9011-0.58982.24440.101-0.09990.27160.1584-0.159-0.0216-0.00450.03730.02670.11480.00050.02360.0983-0.03220.1722159.3758-19.0306221.8227
162.45680.89130.54722.2470.7311.7766-0.02770.05680.15390.02610.0485-0.0548-0.14070.0983-0.020.10370.00480.04360.11390.02330.1344161.6326-20.6314212.845
171.1306-0.07560.9011.74570.94641.77940.2229-0.19970.41540.4849-0.27520.3572-0.2038-0.08080.04140.2226-0.02110.02150.1247-0.05580.2343164.6129-42.7547233.8659
182.70882.84470.25444.71880.60530.80840.1458-0.14510.39360.0296-0.14760.5772-0.1367-0.09640.00550.12780.02370.00910.10240.00050.1928156.5529-50.8757227.0985
192.11351.42530.8552.19570.56671.12570.1514-0.14460.12150.1989-0.14110.0896-0.0161-0.009-0.00070.17020.0010.03210.1233-0.00340.1418164.745-54.8542232.2903
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1065.34070.95191.45153.83253.74075.33070.0062-0.13210.4766-0.0384-0.3149-0.7074-0.79690.26680.26380.74670.0381-0.22460.49720.14480.5321212.6933-13.5958177.9817
1071.38330.06730.28010.74890.26541.5473-0.3743-0.5176-0.06070.55610.2612-0.69070.1828-0.0006-0.10990.16820.2163-0.25760.3822-0.0750.301147.0414-15.5303250.0697
1081.40560.380.10480.15490.15880.6588-0.1082-0.13410.25810.31280.2502-0.85520.11180.2991-0.06460.21950.0861-0.16930.3654-0.14940.5464152.8104-7.6442243.8849
1091.3241-0.22970.66470.45930.42452.31090.1342-0.01650.1298-0.0741-0.0430.1569-0.1193-0.8102-0.09980.20110.05520.01280.4956-0.00070.2402143.387-69.567197.0474
1103.0643-3.5685-0.19027.99240.97250.96410.0344-0.13750.9863-0.3549-0.1637-0.22-0.8796-0.30570.04890.5610.14170.03240.3527-0.04670.385155.0286-51.45292.722
1112.8809-0.474-1.38473.47440.68730.7432-0.0147-0.69680.38840.62230.07770.3029-0.4208-0.5439-0.04020.3740.13840.05670.5685-0.06110.2511150.3699-60.2832101.6718
1122.7445-1.4282-1.19223.02031.07210.62810.0923-0.1230.3657-0.2521-0.04380.1693-0.627-0.6385-0.07840.37250.2130.02540.45910.00810.2679149.3683-61.000488.8786
1132.4292-0.25490.40212.7629-0.03720.40640.26210.05210.0347-0.164-0.00470.5919-0.0608-0.5246-0.1810.79040.2284-0.08911.40080.00650.8471136.0554-62.7328105.1616
1140.38710.50530.16260.66410.2782.26810.2730.03680.2032-0.13420.2159-0.2321-0.67510.5387-0.3820.3241-0.14710.11920.37940.00970.3317174.9221-53.9584122.6714
1151.1479-1.20390.98814.0138-1.06280.84930.06510.27290.385-0.29290.26980.5281-0.5787-0.7736-0.28620.54330.29060.12920.70930.28390.4378150.212-46.2902121.2954
1162.22560.40360.75163.7659-0.90492.17490.28430.54010.2646-0.67110.05270.2423-0.4233-0.4367-0.25160.44840.04360.07240.46810.14340.2669160.8528-53.8534116.7113
1171.5295-0.19130.83330.7797-0.17552.15440.17050.17850.3829-0.12940.16080.0585-0.6162-0.4539-0.33490.37060.03010.10140.29740.11550.3105160.9316-51.5781129.4194
1188.24462.0781-0.41938.65611.18590.23370.27510.40920.8458-0.12040.29660.0999-0.88830.1304-0.55441.1742-0.01570.11680.45210.03650.4298170.9954-43.6894112.8307
1190.72520.1834-0.14251.65091.15432.12360.0785-0.01010.0995-0.17310.1934-0.1477-0.48120.4891-0.25370.268-0.07520.08160.2721-0.00850.2145174.919-68.414391.8847
1202.969-1.80410.72772.9029-0.43262.87410.2436-0.3046-0.3130.09410.0316-0.13980.43850.1297-0.22770.2858-0.0138-0.03410.21030.02540.2172171.0897-86.304796.2787
1211.10440.00710.05841.0688-1.43724.03810.0173-0.14410.00410.3480.09020.166-0.2386-0.3305-0.0740.32930.0110.05860.247-0.03290.1671117.1272-126.2523142.0917
1221.713-0.13870.30463.7752-2.8045.77270.07470.04840.15090.1152-0.08830.17340.0709-0.3327-0.01770.25140.0320.0310.2590.00270.1613117.2102-122.5755130.3524
1230.15870.09840.15120.05790.08620.14450.11550.1374-0.4044-0.08640.0510.00860.6992-0.14090.13171.3233-0.2233-0.04020.1667-0.06990.399116.1005-151.8886135.0784
1243.82332.00731.14674.06241.8450.87160.16830.3484-0.8371-0.2827-0.0262-0.36481.2340.3876-0.07730.990.3003-0.02640.5177-0.02750.3575128.4535-148.5101130.7279
1254.12831.0365-1.05233.7195-0.43150.3935-0.01120.797-0.1912-0.4380.07880.11150.7490.2061-0.04340.70950.15760.01690.38310.00440.2013123.3647-137.9475128.5403
1263.43470.4944-0.82975.68951.01393.4103-0.06751.0628-0.4229-0.97820.13920.43161.0862-0.2298-0.03420.84590.0432-0.07160.5262-0.06420.329120.945-141.0367123.9255
1272.43250.7821-0.37712.48570.79210.4334-0.04770.8639-0.02-0.70770.1070.41750.93030.044-0.02130.6849-0.0444-0.08890.41050.02120.2378119.1612-135.8355129.0148
1281.756-0.113-0.00190.85850.24781.53260.22790.0607-0.2366-0.293-0.2451-0.1851.10050.5076-0.0190.63440.1676-0.00360.35190.04350.1832130.8899-139.7238141.4454
1291.5430.18740.1852.35511.12153.97690.02150.4526-0.4577-0.22860.02150.47340.6184-0.48510.16050.925-0.2558-0.05950.3803-0.11630.3333111.5999-146.6295135.0027
1308.6422.02882.9787.0066-1.38623.36610.32340.45790.3004-0.27260.23340.81380.6446-0.7174-0.48680.7477-0.15630.11580.70340.06920.5727106.4926-134.9114131.0643
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 54 )A2 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 98 )A55 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 111 )A99 - 111
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 125 )A112 - 125
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 137 )A126 - 137
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 147 )A138 - 147
7X-RAY DIFFRACTION7chain 'A' and (resid 148 through 163 )A148 - 163
8X-RAY DIFFRACTION8chain 'A' and (resid 164 through 176 )A164 - 176
9X-RAY DIFFRACTION9chain 'A' and (resid 177 through 187 )A177 - 187
10X-RAY DIFFRACTION10chain 'A' and (resid 188 through 198 )A188 - 198
11X-RAY DIFFRACTION11chain 'A' and (resid 199 through 209 )A199 - 209
12X-RAY DIFFRACTION12chain 'B' and (resid 2 through 23 )B2 - 23
13X-RAY DIFFRACTION13chain 'B' and (resid 24 through 98 )B24 - 98
14X-RAY DIFFRACTION14chain 'B' and (resid 99 through 111 )B99 - 111
15X-RAY DIFFRACTION15chain 'B' and (resid 112 through 163 )B112 - 163
16X-RAY DIFFRACTION16chain 'B' and (resid 164 through 209 )B164 - 209
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 23 )C2 - 23
18X-RAY DIFFRACTION18chain 'C' and (resid 24 through 54 )C24 - 54
19X-RAY DIFFRACTION19chain 'C' and (resid 55 through 98 )C55 - 98
20X-RAY DIFFRACTION20chain 'C' and (resid 99 through 111 )C99 - 111
21X-RAY DIFFRACTION21chain 'C' and (resid 112 through 125 )C112 - 125
22X-RAY DIFFRACTION22chain 'C' and (resid 126 through 137 )C126 - 137
23X-RAY DIFFRACTION23chain 'C' and (resid 138 through 147 )C138 - 147
24X-RAY DIFFRACTION24chain 'C' and (resid 148 through 163 )C148 - 163
25X-RAY DIFFRACTION25chain 'C' and (resid 164 through 187 )C164 - 187
26X-RAY DIFFRACTION26chain 'C' and (resid 188 through 198 )C188 - 198
27X-RAY DIFFRACTION27chain 'C' and (resid 199 through 209 )C199 - 209
28X-RAY DIFFRACTION28chain 'D' and (resid 2 through 23 )D2 - 23
29X-RAY DIFFRACTION29chain 'D' and (resid 24 through 98 )D24 - 98
30X-RAY DIFFRACTION30chain 'D' and (resid 99 through 163 )D99 - 163
31X-RAY DIFFRACTION31chain 'D' and (resid 164 through 208 )D164 - 208
32X-RAY DIFFRACTION32chain 'E' and (resid 2 through 111 )E2 - 111
33X-RAY DIFFRACTION33chain 'E' and (resid 112 through 209 )E112 - 209
34X-RAY DIFFRACTION34chain 'F' and (resid 2 through 111 )F2 - 111
35X-RAY DIFFRACTION35chain 'F' and (resid 112 through 163 )F112 - 163
36X-RAY DIFFRACTION36chain 'F' and (resid 164 through 209 )F164 - 209
37X-RAY DIFFRACTION37chain 'G' and (resid 2 through 98 )G2 - 98
38X-RAY DIFFRACTION38chain 'G' and (resid 99 through 147 )G99 - 147
39X-RAY DIFFRACTION39chain 'G' and (resid 148 through 209 )G148 - 209
40X-RAY DIFFRACTION40chain 'H' and (resid 2 through 23 )H2 - 23
41X-RAY DIFFRACTION41chain 'H' and (resid 24 through 54 )H24 - 54
42X-RAY DIFFRACTION42chain 'H' and (resid 55 through 83 )H55 - 83
43X-RAY DIFFRACTION43chain 'H' and (resid 84 through 98 )H84 - 98
44X-RAY DIFFRACTION44chain 'H' and (resid 99 through 111 )H99 - 111
45X-RAY DIFFRACTION45chain 'H' and (resid 112 through 124 )H112 - 124
46X-RAY DIFFRACTION46chain 'H' and (resid 125 through 137 )H125 - 137
47X-RAY DIFFRACTION47chain 'H' and (resid 138 through 147 )H138 - 147
48X-RAY DIFFRACTION48chain 'H' and (resid 148 through 176 )H148 - 176
49X-RAY DIFFRACTION49chain 'H' and (resid 177 through 187 )H177 - 187
50X-RAY DIFFRACTION50chain 'H' and (resid 188 through 198 )H188 - 198
51X-RAY DIFFRACTION51chain 'H' and (resid 199 through 209 )H199 - 209
52X-RAY DIFFRACTION52chain 'I' and (resid 2 through 98 )I2 - 98
53X-RAY DIFFRACTION53chain 'I' and (resid 99 through 163 )I99 - 163
54X-RAY DIFFRACTION54chain 'I' and (resid 164 through 212 )I164 - 212
55X-RAY DIFFRACTION55chain 'J' and (resid 2 through 111 )J2 - 111
56X-RAY DIFFRACTION56chain 'J' and (resid 112 through 163 )J112 - 163
57X-RAY DIFFRACTION57chain 'J' and (resid 164 through 212 )J164 - 212
58X-RAY DIFFRACTION58chain 'K' and (resid 2 through 98 )K2 - 98
59X-RAY DIFFRACTION59chain 'K' and (resid 99 through 147 )K99 - 147
60X-RAY DIFFRACTION60chain 'K' and (resid 148 through 198 )K148 - 198
61X-RAY DIFFRACTION61chain 'K' and (resid 199 through 209 )K199 - 209
62X-RAY DIFFRACTION62chain 'L' and (resid 2 through 23 )L2 - 23
63X-RAY DIFFRACTION63chain 'L' and (resid 24 through 54 )L24 - 54
64X-RAY DIFFRACTION64chain 'L' and (resid 55 through 83 )L55 - 83
65X-RAY DIFFRACTION65chain 'L' and (resid 84 through 98 )L84 - 98
66X-RAY DIFFRACTION66chain 'L' and (resid 99 through 111 )L99 - 111
67X-RAY DIFFRACTION67chain 'L' and (resid 112 through 125 )L112 - 125
68X-RAY DIFFRACTION68chain 'L' and (resid 126 through 137 )L126 - 137
69X-RAY DIFFRACTION69chain 'L' and (resid 138 through 163 )L138 - 163
70X-RAY DIFFRACTION70chain 'L' and (resid 164 through 198 )L164 - 198
71X-RAY DIFFRACTION71chain 'L' and (resid 199 through 211 )L199 - 211
72X-RAY DIFFRACTION72chain 'M' and (resid 2 through 98 )M2 - 98
73X-RAY DIFFRACTION73chain 'M' and (resid 99 through 163 )M99 - 163
74X-RAY DIFFRACTION74chain 'M' and (resid 164 through 187 )M164 - 187
75X-RAY DIFFRACTION75chain 'M' and (resid 188 through 209 )M188 - 209
76X-RAY DIFFRACTION76chain 'N' and (resid 2 through 111 )N2 - 111
77X-RAY DIFFRACTION77chain 'N' and (resid 112 through 208 )N112 - 208
78X-RAY DIFFRACTION78chain 'O' and (resid 2 through 98 )O2 - 98
79X-RAY DIFFRACTION79chain 'O' and (resid 99 through 163 )O99 - 163
80X-RAY DIFFRACTION80chain 'O' and (resid 164 through 209 )O164 - 209
81X-RAY DIFFRACTION81chain 'P' and (resid 2 through 98 )P2 - 98
82X-RAY DIFFRACTION82chain 'P' and (resid 99 through 137 )P99 - 137
83X-RAY DIFFRACTION83chain 'P' and (resid 138 through 163 )P138 - 163
84X-RAY DIFFRACTION84chain 'P' and (resid 164 through 209 )P164 - 209
85X-RAY DIFFRACTION85chain 'Q' and (resid 3 through 83 )Q3 - 83
86X-RAY DIFFRACTION86chain 'Q' and (resid 84 through 208 )Q84 - 208
87X-RAY DIFFRACTION87chain 'R' and (resid 2 through 23 )R2 - 23
88X-RAY DIFFRACTION88chain 'R' and (resid 24 through 54 )R24 - 54
89X-RAY DIFFRACTION89chain 'R' and (resid 55 through 83 )R55 - 83
90X-RAY DIFFRACTION90chain 'R' and (resid 84 through 98 )R84 - 98
91X-RAY DIFFRACTION91chain 'R' and (resid 99 through 111 )R99 - 111
92X-RAY DIFFRACTION92chain 'R' and (resid 112 through 125 )R112 - 125
93X-RAY DIFFRACTION93chain 'R' and (resid 126 through 137 )R126 - 137
94X-RAY DIFFRACTION94chain 'R' and (resid 138 through 163 )R138 - 163
95X-RAY DIFFRACTION95chain 'R' and (resid 164 through 187 )R164 - 187
96X-RAY DIFFRACTION96chain 'R' and (resid 188 through 200 )R188 - 200
97X-RAY DIFFRACTION97chain 'S' and (resid 2 through 23 )S2 - 23
98X-RAY DIFFRACTION98chain 'S' and (resid 24 through 54 )S24 - 54
99X-RAY DIFFRACTION99chain 'S' and (resid 55 through 83 )S55 - 83
100X-RAY DIFFRACTION100chain 'S' and (resid 84 through 111 )S84 - 111
101X-RAY DIFFRACTION101chain 'S' and (resid 112 through 125 )S112 - 125
102X-RAY DIFFRACTION102chain 'S' and (resid 126 through 137 )S126 - 137
103X-RAY DIFFRACTION103chain 'S' and (resid 138 through 163 )S138 - 163
104X-RAY DIFFRACTION104chain 'S' and (resid 164 through 187 )S164 - 187
105X-RAY DIFFRACTION105chain 'S' and (resid 188 through 198 )S188 - 198
106X-RAY DIFFRACTION106chain 'S' and (resid 199 through 208 )S199 - 208
107X-RAY DIFFRACTION107chain 'T' and (resid 2 through 111 )T2 - 111
108X-RAY DIFFRACTION108chain 'T' and (resid 112 through 208 )T112 - 208
109X-RAY DIFFRACTION109chain 'U' and (resid 2 through 111 )U2 - 111
110X-RAY DIFFRACTION110chain 'U' and (resid 112 through 124 )U112 - 124
111X-RAY DIFFRACTION111chain 'U' and (resid 125 through 163 )U125 - 163
112X-RAY DIFFRACTION112chain 'U' and (resid 164 through 198 )U164 - 198
113X-RAY DIFFRACTION113chain 'U' and (resid 199 through 208 )U199 - 208
114X-RAY DIFFRACTION114chain 'V' and (resid 2 through 98 )V2 - 98
115X-RAY DIFFRACTION115chain 'V' and (resid 99 through 124 )V99 - 124
116X-RAY DIFFRACTION116chain 'V' and (resid 125 through 163 )V125 - 163
117X-RAY DIFFRACTION117chain 'V' and (resid 164 through 198 )V164 - 198
118X-RAY DIFFRACTION118chain 'V' and (resid 199 through 208 )V199 - 208
119X-RAY DIFFRACTION119chain 'W' and (resid 2 through 83 )W2 - 83
120X-RAY DIFFRACTION120chain 'W' and (resid 84 through 209 )W84 - 209
121X-RAY DIFFRACTION121chain 'X' and (resid 2 through 54 )X2 - 54
122X-RAY DIFFRACTION122chain 'X' and (resid 55 through 83 )X55 - 83
123X-RAY DIFFRACTION123chain 'X' and (resid 84 through 111 )X84 - 111
124X-RAY DIFFRACTION124chain 'X' and (resid 112 through 125 )X112 - 125
125X-RAY DIFFRACTION125chain 'X' and (resid 126 through 137 )X126 - 137
126X-RAY DIFFRACTION126chain 'X' and (resid 138 through 147 )X138 - 147
127X-RAY DIFFRACTION127chain 'X' and (resid 148 through 163 )X148 - 163
128X-RAY DIFFRACTION128chain 'X' and (resid 164 through 187 )X164 - 187
129X-RAY DIFFRACTION129chain 'X' and (resid 188 through 198 )X188 - 198
130X-RAY DIFFRACTION130chain 'X' and (resid 199 through 209 )X199 - 209

+
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

+
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

+
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。

-
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