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- PDB-9iyk: Crystal structure of hSOD1 in C121 space group -

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基本情報

登録情報
データベース: PDB / ID: 9iyk
タイトルCrystal structure of hSOD1 in C121 space group
要素Superoxide dismutase [Cu-Zn]
キーワードOXIDOREDUCTASE / hSOD1 / SOD1 / superoxide dismutase (Cu-Zn)
機能・相同性
機能・相同性情報


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / myeloid cell homeostasis / regulation of GTPase activity / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / cellular response to ATP / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / cellular response to cadmium ion / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / placenta development / response to amphetamine / thymus development / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily
類似検索 - ドメイン・相同性
ACETATE ION / COPPER (II) ION / Superoxide dismutase [Cu-Zn]
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.34 Å
データ登録者Yapici, I. / DeMirci, H.
資金援助 トルコ, 1件
組織認可番号国
Other government122Z429 トルコ
引用ジャーナル: Int J Mol Sci / 年: 2025
タイトル: Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions.
著者: Yapici, I. / Tokur, A.G. / Sever, B. / Ciftci, H. / Basak, A.N. / DeMirci, H.
履歴
登録2024年7月30日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年8月14日Provider: repository / タイプ: Initial release
改定 1.12024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
改定 1.22025年5月7日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
改定 1.32025年5月28日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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 [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)196,44145
ポリマ－194,20812
非ポリマー2,23333
水8,881493
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,90510
ポリマ－32,3682
非ポリマー5378
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-27 kcal/mol
Surface area14060 Å2
手法PISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,8409
ポリマ－32,3682
非ポリマー4727
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-24 kcal/mol
Surface area14020 Å2
手法PISA
3
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,6266
ポリマ－32,3682
非ポリマー2584
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-17 kcal/mol
Surface area13930 Å2
手法PISA
4
F: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,7227
ポリマ－32,3682
非ポリマー3545
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-9 kcal/mol
Surface area13890 Å2
手法PISA
5
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,6266
ポリマ－32,3682
非ポリマー2584
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-17 kcal/mol
Surface area13670 Å2
手法PISA
6
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,7227
ポリマ－32,3682
非ポリマー3545
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area13830 Å2
手法PISA
単位格子
Length a, b, c (Å)178.190, 138.250, 112.930
Angle α, β, γ (deg.)90.00, 129.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11F-339-

HOH

21B-343-

HOH

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要素

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タンパク質 , 1種, 12分子 ACKFEDBGILJH

#1: タンパク質
Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


分子量: 16183.982 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SOD1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P00441, superoxide dismutase

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非ポリマー , 5種, 526分子

#2: 化合物
ChemComp-CU / COPPER (II) ION


分子量: 63.546 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Cu / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 13 / 由来タイプ: 合成 / 式: Zn / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C2H3O2 / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 4 / 由来タイプ: 合成 / 式: SO4 / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 493 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
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: 2.83 Å3/Da / 溶媒含有率: 56.46 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: Ammonium sulfate, sodium acetate

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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: I03 / 波長: 0.98 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2023年12月1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: 0.98 Å / 相対比: 1
反射解像度: 2.34→56.47 Å / Num. obs: 88500 / % possible obs: 99.2 % / 冗長度: 7.13 % / CC1/2: 0.939 / Net I/σ(I): 9
反射 シェル解像度: 2.34→2.38 Å / Num. unique obs: 4366 / CC1/2: 0.237

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.20.1_4487: ???)精密化
xia2データ削減
xia2データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.34→48.92 Å / SU ML: 0.41 / 交差検証法: FREE R-VALUE / σ(F): 0 / 位相誤差: 33.72 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2632 3831 4.98 %
Rwork0.1981 --
obs0.2014 77004 86.28 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.34→48.92 Å
タンパク質核酸リガンド溶媒全体
原子数13364 0 55 493 13912
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00414160
X-RAY DIFFRACTIONf_angle_d0.63419249
X-RAY DIFFRACTIONf_dihedral_angle_d13.3545119
X-RAY DIFFRACTIONf_chiral_restr0.052096
X-RAY DIFFRACTIONf_plane_restr0.0042624
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.370.39061100.35472022X-RAY DIFFRACTION66
2.37-2.40.42831150.36682192X-RAY DIFFRACTION68
2.4-2.430.43521210.35952140X-RAY DIFFRACTION70
2.43-2.470.45181210.34572286X-RAY DIFFRACTION72
2.47-2.510.35661220.33032318X-RAY DIFFRACTION73
2.51-2.540.4221290.31942268X-RAY DIFFRACTION74
2.54-2.590.40281220.31332374X-RAY DIFFRACTION76
2.59-2.630.39251300.3052418X-RAY DIFFRACTION76
2.63-2.680.4381190.32032325X-RAY DIFFRACTION75
2.68-2.730.35321210.29922436X-RAY DIFFRACTION79
2.73-2.790.35361460.29812598X-RAY DIFFRACTION82
2.79-2.850.34751350.2852690X-RAY DIFFRACTION86
2.85-2.910.38911440.28872745X-RAY DIFFRACTION87
2.91-2.990.30171460.26052788X-RAY DIFFRACTION90
2.99-3.070.31731460.2482834X-RAY DIFFRACTION90
3.07-3.160.28381540.23482969X-RAY DIFFRACTION94
3.16-3.260.3211530.22282966X-RAY DIFFRACTION94
3.26-3.370.29521510.22382989X-RAY DIFFRACTION95
3.37-3.510.29211560.21713008X-RAY DIFFRACTION96
3.51-3.670.25751550.19452993X-RAY DIFFRACTION96
3.67-3.860.29161450.17562971X-RAY DIFFRACTION95
3.86-4.10.21521680.163077X-RAY DIFFRACTION98
4.1-4.420.19751620.12623118X-RAY DIFFRACTION99
4.42-4.870.19351630.12113136X-RAY DIFFRACTION99
4.87-5.570.17461620.13793155X-RAY DIFFRACTION100
5.57-7.010.20911650.1593155X-RAY DIFFRACTION99
7.02-48.920.20221700.15713202X-RAY DIFFRACTION100
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)
13.48350.87842.44961.89951.70695.92850.4229-0.8880.39140.619-0.25010.09050.21190.1074-0.31190.7154-0.42350.25230.5874-0.31460.56529.9763-10.781137.1723
23.0537-0.7463-0.4194.41960.03882.27270.3467-0.70090.43960.4875-0.02590.5845-0.13720.1238-0.32490.4833-0.25760.10890.4349-0.10830.418322.3381-20.172531.7731
32.43160.11490.00371.14160.36551.19330.3368-0.67950.03470.3918-0.32770.27840.05370.0635-0.00130.5081-0.28320.12790.5379-0.13590.364324.3883-19.890732.6954
42.3464-0.1605-1.49123.4254-0.36783.8076-0.5318-0.7152-0.8697-0.2911-0.3134-0.26510.76971.35320.66810.64680.27130.29440.83270.38480.657440.8067-53.285326.6947
56.22-0.9463-0.47774.79660.62753.7251-0.1985-0.0984-0.4442-0.4708-0.1716-0.25520.20070.54690.27380.32780.02370.01150.29620.02110.194132.8194-42.499521.1979
64.9722-2.01071.30456.0095-3.88373.1978-0.15960.2151-1.5786-0.8968-0.2282-0.23111.06430.90780.33190.83990.24510.41490.59740.20770.817540.9319-54.971114.6801
72.3381-0.10252.07394.8118-1.12175.7457-0.2295-0.5633-0.51060.0011-0.20520.02650.02060.31660.3570.26920.12080.1050.49850.1190.285733.3886-44.087322.2619
84.44984.398-0.12874.37690.08774.30770.1067-0.14750.7106-0.2464-0.15540.4224-0.58850.01910.04340.44920.13580.06940.47240.03980.45259.5772-43.9416-10.8143
93.84960.35780.43675.4492.51435.4537-0.3237-0.64770.04310.2046-0.04570.1283-0.1152-0.2620.33870.28390.15870.07320.42850.05450.292853.5722-46.7237-2.8357
107.3033-6.7814-6.35866.29665.88915.8563-0.8892-2.01140.55682.03671.1828-1.13060.40251.2174-0.27090.60250.1928-0.03810.67950.00030.464265.5405-41.3064-1.0267
115.2048-0.89950.60751.6261.11611.0821-0.2133-0.3357-0.38040.29230.03120.19540.2741-0.04980.16130.44950.19290.10450.40020.17120.396752.1569-51.24920.4909
126.9931-2.44065.01871.2596-1.16435.08310.10250.71640.2808-0.4832-0.4138-0.3493-0.11030.35650.30160.82820.49620.09350.90230.16770.41820.5423-15.0275-18.8305
132.0053-1.31671.31953.6561-2.83954.4296-0.06710.06750.08240.3532-0.1117-0.1214-0.55850.03490.20790.70970.3928-0.0240.77890.13590.457415.79-9.9472-15.4107
143.1741.243-2.88.9573.09944.6606-0.2638-0.27660.79351.33630.166-0.5137-0.9528-0.28560.07381.15730.3956-0.0730.80590.1650.548112.17143.194-9.9255
154.7952-1.73082.72923.7002-2.64515.00990.22720.65060.3323-0.0383-0.1901-0.3055-0.25650.09120.13060.62130.45740.03120.67460.24860.519511.2872-3.2646-20.0265
161.87590.71562.10870.27250.81422.4712-0.32930.37550.7263-0.2797-0.2361-0.1539-0.46130.13550.61670.92840.52220.02021.11680.36760.87318.6545-5.3842-24.8437
176.5315-5.42863.13097.9212-4.45552.5082-0.6035-0.68631.61441.30620.0737-1.2834-0.73650.23840.50280.91440.3325-0.09320.71950.13470.987224.5946-2.9179-9.3673
183.4697-1.97251.49282.4469-1.34981.4289-0.0445-0.0792-0.08580.37080.17190.1773-0.2816-0.0915-0.07420.69130.55780.06460.72810.2910.44539.3402-7.9391-13.836
194.8344-2.3910.60964.0373-2.23052.7270.0730.45720.1242-0.0663-0.2065-0.0349-0.6094-0.33030.10830.5710.2941-0.04670.53620.02030.366625.5826-25.6496-3.5273
205.428-1.11320.61132.2574-1.26143.2330.09330.141-0.27550.2169-0.3949-0.3196-0.13490.34930.29750.55630.26-0.08310.45550.04150.409733.8794-30.11081.223
218.7713-7.02255.59069.0554-6.49174.9292-0.68930.09722.33120.8532-0.191-1.7978-2.43550.04940.93530.82890.1484-0.11750.49350.03560.716932.8973-15.9608-0.9041
226.4809-4.60712.33786.0084-1.73630.84930.63331.1231-0.0363-0.4219-0.6649-0.0955-0.2808-0.16240.00110.56460.3070.04950.70760.07560.335832.755-31.6208-7.0262
236.2171.8435-3.29813.4756-4.36555.6690.2193-0.8525-0.12520.4569-0.37960.1077-0.30770.39930.05830.68040.10590.25920.61550.30720.528724.091-48.04842.5466
240.69550.0403-0.22150.6579-0.57491.1739-0.028-0.3412-0.2148-0.0066-0.2179-0.21630.14370.5019-0.03150.7940.50610.29481.59181.01090.956732.018-58.685449.1998
250.40860.0835-0.55991.374-1.31731.9119-0.3669-0.708-0.60980.1993-0.2783-0.3180.44910.94610.13930.82560.3840.26931.23080.71370.703927.5029-57.579348.561
264.45810.62560.28736.37880.18072.45070.1782-0.10270.02260.1389-0.1823-0.3208-0.23870.43990.00910.304-0.15960.07190.3757-0.05250.31944.4201-13.586717.7427
273.44470.84540.18114.37870.4861.31240.074-0.29540.4280.1107-0.0499-0.4647-0.22830.3344-0.01510.515-0.31790.0760.5663-0.10730.475750.5182-7.368622.1513
285.5649-2.5768-7.23039.34762.99099.410.4277-1.89940.36541.3053-0.1954-1.04210.06371.1433-0.23180.6086-0.3134-0.02620.6493-0.07110.497949.3807-17.784728.539
292.7761.8789-0.37572.45710.33730.84940.1517-0.29450.36930.06390.0636-0.1235-0.24740.4796-0.09550.654-0.4140.17110.4574-0.23220.666649.7115-2.338222.0484
304.34522.97150.31954.30880.39451.78030.08930.0788-1.00210.0339-0.0658-0.95220.12240.3013-0.33350.7161-0.55260.02560.7243-0.32150.80452.5552-42.043625.4798
317.83513.37941.04194.97071.42692.92770.3461-0.8084-0.88940.5164-0.2548-0.32350.12170.0415-0.08490.725-0.4068-0.01740.6909-0.04870.59090.4676-36.981635.2521
324.06643.30633.11857.9465.06976.57940.3609-0.6441-0.61640.7744-0.4925-0.5590.2175-0.33550.06610.6075-0.44950.09380.8928-0.23760.6954-2.8066-36.870436.8141
334.2589-1.8189-1.89615.4706-2.81169.0299-0.4013-0.0894-0.34770.20710.14130.43461.2271-0.75530.27261.0048-0.45370.17181.2164-0.13370.4356-2.9995-21.363462.4527
345.3849-2.2272-1.85763.50540.92582.32120.44820.07740.2623-0.53850.0732-0.395-0.1584-0.2295-0.52030.8994-0.40790.24241.0722-0.16820.50497.8952-13.532157.3496
354.476-0.1367-4.74762.40050.02527.0643-0.3369-0.2571-0.2296-0.05630.1837-0.06930.8686-0.13470.13610.914-0.41810.20261.0351-0.18730.475.9921-17.901755.9719
365.3414-0.2829-0.27463.9651.5962.8102-0.1819-0.862-0.46950.35950.1925-0.41020.19040.32740.19510.49610.28050.13950.72410.26440.520575.821-59.3696-7.0364
374.8238-0.3861-0.30423.13171.10752.3704-0.06440.30680.2057-0.1918-0.253-0.5232-0.0862-0.03010.17210.47570.18360.19540.52310.23980.544377.1936-53.484-19.8284
385.8744-4.8439-0.9234.4558-0.98536.7476-0.1391-0.2160.517-0.0994-0.3322-2.2376-0.29030.8780.43090.49820.17590.16320.81790.34380.864187.299-51.075-17.6761
393.665-3.77580.10559.62730.25723.0799-0.3922-0.4435-0.96030.5397-0.03640.20030.54260.32360.40020.590.32150.28760.73430.32540.792280.9958-68.2445-14.0052
407.2507-7.259-0.20058.10551.57736.96880.08590.1871.7392-0.15470.3292-1.5547-0.57091.0146-0.39760.37920.07580.09180.67410.10280.690879.5108-47.7613-7.8166
411.659-0.441-0.37740.86810.40960.3576-0.09060.15150.1165-0.2582-0.1953-0.3155-0.02380.2568-0.12940.59610.36230.20990.73970.43980.512278.3399-56.5274-22.2089
425.9081-0.2807-3.86976.62961.20132.96430.313-0.09051.11240.1470.6709-0.213-0.73310.8004-1.02090.7499-0.21830.22511.101-0.09560.5651.5348-4.078979.8145
436.2662-0.3688-3.01835.90661.34338.8718-0.01120.0860.50290.5060.65620.00840.38540.1152-0.5730.7935-0.25820.27951.0466-0.04330.493-4.3671-9.797785.4604
445.76840.3843-6.49921.59210.09997.4986-0.00710.75310.2601-0.17080.4132-0.00410.49850.2726-0.33730.7462-0.25830.11210.9369-0.08070.4138-5.5396-10.613484.2118
455.35111.73780.91777.21270.25835.55060.349-0.3307-0.59680.4169-0.3115-0.1636-0.1654-0.0439-0.02290.7342-0.4064-0.08750.5286-0.1210.6162-16.973-51.215127.5619
465.01580.25713.04317.0649-2.34738.90290.9561-0.8936-1.4810.5441-0.5524-0.42211.39280.0477-0.43221.001-0.3748-0.17510.77240.17961.0252-17.9552-59.944232.6475
472.23641.99950.43012.7503-0.04540.4413-0.32970.5634-0.0221-0.59020.6251-0.5152-0.19480.507-0.02490.7249-0.56950.26790.887-0.3491.198-12.8406-54.54216.8349
487.86777.3997-4.36238.5941-4.57882.81010.2327-0.1924-0.55550.2406-0.2219-0.7159-0.34120.64030.00291.1219-0.3638-0.0321.3624-0.74762.8872-9.587-69.422317.9276
491.0642-0.8665-0.94391.10611.79313.45820.12620.5904-1.92480.15240.3837-1.71371.02540.2762-0.52820.7865-0.35030.2730.8235-0.61721.7711-12.1826-68.322619.4446
504.22992.86081.83386.32531.46063.4994-0.08640.1109-0.1962-0.28780.02130.36130.0241-0.17810.06350.6618-0.43420.02390.621-0.20180.9027-27.1664-57.915723.0086
513.64613.69592.15593.77162.02312.29910.34340.2257-1.78490.3690.2006-1.92810.72840.4282-0.43530.9363-0.3573-0.19630.7337-0.23531.9609-6.6257-61.939529.1135
523.62033.07883.10284.61381.77743.0243-0.38621.1202-1.0535-1.01660.7473-0.85280.03640.4201-0.3121.0085-0.66230.3050.9818-0.48120.9702-15.053-58.886814.7693
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 153 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 36 )
5X-RAY DIFFRACTION5chain 'C' and (resid 37 through 85 )
6X-RAY DIFFRACTION6chain 'C' and (resid 86 through 101 )
7X-RAY DIFFRACTION7chain 'C' and (resid 102 through 153 )
8X-RAY DIFFRACTION8chain 'K' and (resid 2 through 28 )
9X-RAY DIFFRACTION9chain 'K' and (resid 29 through 101 )
10X-RAY DIFFRACTION10chain 'K' and (resid 102 through 115 )
11X-RAY DIFFRACTION11chain 'K' and (resid 116 through 153 )
12X-RAY DIFFRACTION12chain 'F' and (resid 1 through 22 )
13X-RAY DIFFRACTION13chain 'F' and (resid 23 through 65 )
14X-RAY DIFFRACTION14chain 'F' and (resid 66 through 75 )
15X-RAY DIFFRACTION15chain 'F' and (resid 76 through 93 )
16X-RAY DIFFRACTION16chain 'F' and (resid 94 through 102 )
17X-RAY DIFFRACTION17chain 'F' and (resid 103 through 112 )
18X-RAY DIFFRACTION18chain 'F' and (resid 113 through 153 )
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 65 )
20X-RAY DIFFRACTION20chain 'E' and (resid 66 through 101 )
21X-RAY DIFFRACTION21chain 'E' and (resid 102 through 115 )
22X-RAY DIFFRACTION22chain 'E' and (resid 116 through 153 )
23X-RAY DIFFRACTION23chain 'D' and (resid -2 through 36 )
24X-RAY DIFFRACTION24chain 'D' and (resid 37 through 85 )
25X-RAY DIFFRACTION25chain 'D' and (resid 86 through 153 )
26X-RAY DIFFRACTION26chain 'B' and (resid -2 through 48 )
27X-RAY DIFFRACTION27chain 'B' and (resid 49 through 101 )
28X-RAY DIFFRACTION28chain 'B' and (resid 102 through 115 )
29X-RAY DIFFRACTION29chain 'B' and (resid 116 through 153 )
30X-RAY DIFFRACTION30chain 'G' and (resid 2 through 36 )
31X-RAY DIFFRACTION31chain 'G' and (resid 37 through 107 )
32X-RAY DIFFRACTION32chain 'G' and (resid 108 through 153 )
33X-RAY DIFFRACTION33chain 'I' and (resid 1 through 36 )
34X-RAY DIFFRACTION34chain 'I' and (resid 37 through 75 )
35X-RAY DIFFRACTION35chain 'I' and (resid 76 through 153 )
36X-RAY DIFFRACTION36chain 'L' and (resid 1 through 36 )
37X-RAY DIFFRACTION37chain 'L' and (resid 37 through 75 )
38X-RAY DIFFRACTION38chain 'L' and (resid 76 through 85 )
39X-RAY DIFFRACTION39chain 'L' and (resid 86 through 101 )
40X-RAY DIFFRACTION40chain 'L' and (resid 102 through 115 )
41X-RAY DIFFRACTION41chain 'L' and (resid 116 through 153 )
42X-RAY DIFFRACTION42chain 'J' and (resid 1 through 48 )
43X-RAY DIFFRACTION43chain 'J' and (resid 49 through 101 )
44X-RAY DIFFRACTION44chain 'J' and (resid 102 through 153 )
45X-RAY DIFFRACTION45chain 'H' and (resid 1 through 22 )
46X-RAY DIFFRACTION46chain 'H' and (resid 23 through 36 )
47X-RAY DIFFRACTION47chain 'H' and (resid 37 through 65 )
48X-RAY DIFFRACTION48chain 'H' and (resid 66 through 75 )
49X-RAY DIFFRACTION49chain 'H' and (resid 76 through 85 )
50X-RAY DIFFRACTION50chain 'H' and (resid 86 through 101 )
51X-RAY DIFFRACTION51chain 'H' and (resid 102 through 115 )
52X-RAY DIFFRACTION52chain 'H' and (resid 116 through 153 )

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万見について

-
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