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- PDB-6swu: Crystal structure of the TPR domain of KLC1 in complex with an en... -

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基本情報

登録情報
データベース: PDB / ID: 6swu
タイトルCrystal structure of the TPR domain of KLC1 in complex with an engineered high-affinity cargo peptide.
要素Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
キーワードMOTOR PROTEIN / PROTEIN COMPLEX / PROTEIN ENGINEERING / CARGO RECOGNITION
機能・相同性
機能・相同性情報


kinesin complex / microtubule / cytoplasm
類似検索 - 分子機能
Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / Kinesin light chain
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.849 Å
データ登録者Chegkazi, M.S. / Steiner, R.A.
資金援助 英国, 1件
組織認可番号
Biotechnology and Biological Sciences Research CouncilBB/S000828/1, BB/S000917/1 英国
引用ジャーナル: Cell Chem Biol / : 2021
タイトル: Fragment-linking peptide design yields a high-affinity ligand for microtubule-based transport.
著者: Cross, J.A. / Chegkazi, M.S. / Steiner, R.A. / Woolfson, D.N. / Dodding, M.P.
履歴
登録2019年9月23日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年9月30日Provider: repository / タイプ: Initial release
改定 2.02021年8月18日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / database_2 / entity / entity_poly / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id ..._atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _entity_poly.pdbx_strand_id / _pdbx_database_status.pdb_format_compatible / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_main_chain_plane.auth_asym_id / _pdbx_validate_peptide_omega.auth_asym_id_1 / _pdbx_validate_peptide_omega.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id
改定 2.12021年9月29日Group: Data collection / Database references / カテゴリ: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first / _diffrn_source.pdbx_synchrotron_site
改定 2.22024年1月24日Group: Data collection / Derived calculations / Refinement description
カテゴリ: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site

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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: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
B: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
C: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
D: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
E: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
F: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)228,27517
ポリマ-227,5046
非ポリマー77111
1,65792
1
A: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
B: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,0474
ポリマ-75,8352
非ポリマー2122
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-14 kcal/mol
Surface area26870 Å2
手法PISA
2
C: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
D: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,2699
ポリマ-75,8352
非ポリマー4347
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-14 kcal/mol
Surface area26460 Å2
手法PISA
3
E: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
F: Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)75,9594
ポリマ-75,8352
非ポリマー1242
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-14 kcal/mol
Surface area26320 Å2
手法PISA
単位格子
Length a, b, c (Å)101.732, 107.532, 222.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11Chains A B
22Chains A C
33Chains A D
44Chains A E
55Chains A F
66Chains B C
77Chains B D
88Chains B E
99Chains B F
1010Chains C D
1111Chains C E
1212Chains C F
1313Chains D E
1414Chains D F
1515Chains E F

NCSアンサンブル:
ID詳細
1AB
2AC
3AD
4AE
5AF
6BC
7BD
8BE
9BF
10CD
11CE
12CF
13DE
14DF
15EF

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要素

#1: タンパク質
Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI


分子量: 37917.391 Da / 分子数: 6 / 由来タイプ: 組換発現
詳細: aa (1-4) are cloning artifacts. aa (5-296) correspond to residues (205-496) of Uniprot entry Q5UE59 aa (297-327) is an engineered flexible linker. aa (328-343) is an engineered recognition ...詳細: aa (1-4) are cloning artifacts. aa (5-296) correspond to residues (205-496) of Uniprot entry Q5UE59 aa (297-327) is an engineered flexible linker. aa (328-343) is an engineered recognition peptide. It is a fusion peptide of short TorsinA, JIP1, and SKIP protein segments. Residues (328-331, TVFT) correspond to residues (321-324) of Uniprot entry O14656. Residues (332-336, TEDIY) correspond to residues (705-709) of Uniprot entry Q9UQF2. Residues (337-343, EWDDSAI) correspond to residues (206-212) of Uniprot entry Q8IWE5.
由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Klc1, Kns2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q5UE59
#2: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 2 / 由来タイプ: 合成 / : C4H10O3
#3: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 9 / 由来タイプ: 合成 / : C2H6O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 92 / 由来タイプ: 天然 / : 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: 2.68 Å3/Da / 溶媒含有率: 54.04 %
結晶化温度: 300 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 9 / 詳細: 0.1 M MIB buffer pH 9.0, 25% PEG 1500

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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: 0.97625 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2019年6月23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: 0.97625 Å / 相対比: 1
反射解像度: 2.849→111.325 Å / Num. obs: 57529 / % possible obs: 99.3 % / 冗長度: 4.47 % / CC1/2: 0.994 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.063 / Rrim(I) all: 0.131 / Net I/σ(I): 8
反射 シェル解像度: 2.85→2.9 Å / 冗長度: 4.42 % / Rmerge(I) obs: 1.543 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2758 / CC1/2: 0.365 / Rpim(I) all: 0.889 / Rrim(I) all: 1.791 / % possible all: 97.1

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0253精密化
DIALSデータ削減
DIALSデータスケーリング
REFMAC位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3NF1, 6FV0
解像度: 2.849→111.325 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 36.483 / SU ML: 0.304 / 交差検証法: FREE R-VALUE / ESU R Free: 0.355 / 詳細: Hydrogens have been added in their riding positions
Rfactor反射数%反射
Rfree0.2426 2703 4.707 %
Rwork0.2015 --
all0.203 --
obs-57431 99.18 %
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--3.114 Å20 Å20 Å2
2---2.107 Å20 Å2
3---5.22 Å2
精密化ステップサイクル: LAST / 解像度: 2.849→111.325 Å
タンパク質核酸リガンド溶媒全体
原子数13783 0 50 92 13925
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01314071
X-RAY DIFFRACTIONr_bond_other_d0.0020.01713183
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.65618960
X-RAY DIFFRACTIONr_angle_other_deg1.2691.58530620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84151699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41822.677807
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.874152563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.58115102
X-RAY DIFFRACTIONr_chiral_restr0.0650.21778
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022858
X-RAY DIFFRACTIONr_nbd_refined0.2060.22808
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.211095
X-RAY DIFFRACTIONr_nbtor_refined0.1560.26726
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.27015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2165
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0560.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.217
X-RAY DIFFRACTIONr_nbd_other0.2130.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3070.21
X-RAY DIFFRACTIONr_mcbond_it2.2444.9166853
X-RAY DIFFRACTIONr_mcbond_other2.2434.9156852
X-RAY DIFFRACTIONr_mcangle_it3.6647.378530
X-RAY DIFFRACTIONr_mcangle_other3.6647.3718531
X-RAY DIFFRACTIONr_scbond_it2.6545.2647218
X-RAY DIFFRACTIONr_scbond_other2.6545.2657219
X-RAY DIFFRACTIONr_scangle_it4.367.74710429
X-RAY DIFFRACTIONr_scangle_other4.367.74810430
X-RAY DIFFRACTIONr_lrange_it8.22893.10357616
X-RAY DIFFRACTIONr_lrange_other8.22893.10257616
X-RAY DIFFRACTIONr_ncsr_local_group_10.1150.058905
X-RAY DIFFRACTIONr_ncsr_local_group_20.1070.058998
X-RAY DIFFRACTIONr_ncsr_local_group_30.1130.059013
X-RAY DIFFRACTIONr_ncsr_local_group_40.1170.058858
X-RAY DIFFRACTIONr_ncsr_local_group_50.1030.058898
X-RAY DIFFRACTIONr_ncsr_local_group_60.1070.059002
X-RAY DIFFRACTIONr_ncsr_local_group_70.1050.059034
X-RAY DIFFRACTIONr_ncsr_local_group_80.1160.058841
X-RAY DIFFRACTIONr_ncsr_local_group_90.1070.058927
X-RAY DIFFRACTIONr_ncsr_local_group_100.1080.059041
X-RAY DIFFRACTIONr_ncsr_local_group_110.1120.058830
X-RAY DIFFRACTIONr_ncsr_local_group_120.1020.058881
X-RAY DIFFRACTIONr_ncsr_local_group_130.1140.058890
X-RAY DIFFRACTIONr_ncsr_local_group_140.1020.059003
X-RAY DIFFRACTIONr_ncsr_local_group_150.1110.058907
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)
17.85491.4782-0.347511.4015-4.670810.961-0.11480.40190.0452-0.5059-0.1807-0.7779-0.4360.89870.29550.35630.01090.03030.3433-0.12480.205117.359840.0205-38.4072
210.82277.0829-5.92384.8805-5.25611.497-0.26870.24720.3924-0.1290.10270.148-0.55970.00990.1660.5490.02370.01890.48220.01870.584623.677549.9475-32.8474
35.07680.20630.81589.0978-0.62669.5323-0.04720.468-0.3939-0.12740.0042-0.69610.2670.51880.0430.22610.0516-0.01840.2979-0.07680.264720.645740.1431-23.6197
45.09495.5494-6.75497.0388-5.710711.7321-0.42340.1-0.0336-0.60060.5686-0.22070.21450.6631-0.14520.5038-0.0388-0.05660.46210.06920.492122.015656.8978-21.541
55.0759-0.3437-0.8574.2718-1.57017.2360.0627-0.20140.2469-0.1168-0.0083-0.1725-0.40940.4561-0.05450.1254-0.0859-0.1110.10110.05630.18515.91248.467-6.8317
65.09832.3331-2.75438.3808-4.45126.18040.0307-0.05820.36750.10810.00850.1387-0.4223-0.1533-0.03930.07220.0182-0.05530.0129-0.00510.09880.73543.8390.9132
71.5998-1.08130.00559.5689-3.44735.8380.1349-0.11960.0430.15220.0770.5531-0.2353-0.3014-0.21190.13230.0257-0.02880.2739-0.04220.3696-16.073338.19132.9981
81.80080.386-0.55450.5905-0.07060.1763-0.00740.2397-0.5290.1634-0.20870.28390.0022-0.08460.21610.6458-0.0653-0.02940.7157-0.00780.706-22.726324.73467.7805
96.11225.59886.53536.03984.185610.5727-0.1656-0.1471-0.17030.0671-0.3231-0.5271-0.56230.28880.48870.53440.0228-0.04150.44960.04520.5227-16.540137.1091-13.5123
105.04221.74610.72627.6821-2.21889.82-0.10720.1164-0.0792-0.1978-0.18790.08850.1579-0.12530.29510.06160.05450.01120.0867-0.02750.2434-6.244329.23271.1411
1113.1572-1.81832.24873.22994.11227.03690.45670.2003-0.18830.4391-0.134-0.07850.9732-0.0917-0.32260.6127-0.0021-0.04230.2280.09430.58130.311227.5633-2.7288
127.80580.7146-3.521915.2854-11.053713.73290.03930.17930.0387-0.43250.28050.71020.3603-0.3239-0.31980.2546-0.0136-0.0750.3504-0.12550.247910.226741.7557-13.5823
137.1986-1.01542.69956.4736-1.34698.58630.09290.0625-0.6940.39760.0870.10970.2487-0.6716-0.17980.07420.0020.04720.07650.00860.2105-9.690112.6846-1.3225
148.65961.0019-3.13324.581-2.53315.99520.29760.0614-0.6193-0.1461-0.2098-0.0797-0.0257-0.0561-0.08780.10980.00870.01310.0973-0.01930.1039-18.537213.9636-12.7089
157.8752-0.5168-3.70354.7589-0.90738.7949-0.09630.2916-0.4208-0.47630.08750.11080.31890.03180.00880.2488-0.0261-0.00720.14060.01810.152-21.58420.7586-24.1839
162.9486-0.6043-3.03424.4559-0.041913.0477-0.30660.1763-0.1449-0.08910.08560.8611-0.09420.05710.2210.2262-0.0935-0.01580.13230.01520.1711-24.716231.2267-25.2645
172.6376-0.6449-3.20727.46410.6784.20880.31930.16580.4048-0.94840.06750.4223-0.6715-0.304-0.38680.46320.0571-0.10760.29640.07830.229-23.430239.6207-28.5215
185.88351.2636-2.27916.05670.188211.4928-0.1386-0.10410.4097-0.1138-0.07020.4288-0.1839-0.06520.20880.13280.0435-0.03040.13070.00870.0646-12.292542.9725-33.3696
194.5268-2.3643-2.35795.02123.20868.02020.0706-0.17480.5390.1413-0.1655-0.2617-0.4765-0.0050.09490.4117-0.0575-0.03040.3125-0.04780.3562-2.612656.9795-31.3208
207.2861-1.44960.91042.9929-1.354513.9974-0.4787-0.1067-0.314-0.01740.0764-0.11590.0222-1.3190.40220.5267-0.0987-0.10970.1783-0.12990.61853.452.9695-25.9243
215.8738-0.9884-3.82784.83353.24598.3832-0.1120.1537-0.2603-0.0502-0.0944-0.2030.46570.27860.20640.2478-0.0007-0.05070.2812-0.0270.2257-1.3942.6384-36.6421
222.9741-3.12947.77419.9055-9.82124.5606-0.2354-0.09580.01090.3401-0.0066-0.7456-0.44130.39230.24190.3294-0.0107-0.00860.3288-0.01740.29565.662646.167-33.5628
231.12910.4878-1.90410.2671-0.94193.7234-0.1069-0.2193-0.1452-0.2632-0.094-0.10320.69590.84870.20080.85130.11640.08560.9348-0.08150.7213-4.684732.4773-31.5034
245.31441.47461.04244.05514.666221.91390.2402-0.5755-0.97481.0927-0.2318-0.1381-1.10330.4329-0.00850.657-0.1027-0.0360.32430.04680.3842-16.571426.1704-14.3899
257.31331.83350.80769.3904-0.55147.103-0.07430.41810.1967-0.1497-0.01510.25890.1183-0.29550.08950.0055-0.0040.01040.06430.0720.2309-52.24344.9141-4.8767
267.84454.5783-4.782210.37082.24636.2227-0.3390.2755-0.2386-0.17130.2095-0.12320.243-0.05850.12950.40790.0373-0.05760.5622-0.11130.4404-47.875738.4043-16.7743
279.96651.7629-2.40544.02160.12559.9715-0.2377-0.0071-0.7651-0.094-0.14460.24720.1454-0.33460.38240.0523-0.0033-0.00180.03350.04470.3358-38.165746.4337-8.0738
2814.263510.33483.059120.8222-4.34019.0659-0.5396-0.1096-0.3206-0.71410.2998-0.289-0.0239-0.19170.23980.39690.0551-0.07080.47820.01060.1683-36.907849.8911-24.5441
299.8956-1.43115.41324.4572-2.14976.9408-0.1380.43-0.3311-0.2419-0.0674-0.28410.09780.18250.20540.10220.00050.09060.07490.00680.3048-27.384251.1025-10.5069
308.8348-1.4892.7126.0167-0.55033.0974-0.14930.790.2563-1.14390.1566-0.2943-0.58950.3078-0.00730.3803-0.09370.0630.11170.02760.0846-24.424860.9144-16.551
314.4048-2.07661.946810.1957-0.67026.06780.060.12530.53-0.62540.0116-0.1391-0.9162-0.0256-0.07160.3367-0.1277-0.03740.15680.14060.2715-24.108872.1255-11.6954
326.0549-1.64930.52778.90863.30675.22080.0723-0.11570.6053-0.2076-0.04740.0349-0.4886-0.3821-0.02480.2925-0.09690.0360.15630.09090.2796-19.845580.50242.6476
338.72343.00036.02641.0832.05424.177-0.75541.50660.1061-0.17920.5873-0.1439-0.59891.04170.16810.83420.0284-0.18090.55610.04520.9645-35.342686.289511.0642
344.26821.4452.14524.9235-0.09766.88510.35351.3567-0.09020.3544-0.20450.4715-0.8047-0.56-0.1490.69560.1336-0.06410.9286-0.01770.5808-36.726876.73432.5531
357.60912.25332.1242.45261.20176.526-0.1824-0.3301-0.12290.23720.07770.23630.23990.11430.10470.3606-0.04120.0640.22420.11010.2949-20.716974.356911.6414
3614.52493.82077.731911.55372.012410.20350.3399-1.71640.44510.2746-0.25120.2069-0.1045-1.1164-0.08870.25440.00190.1480.2509-0.01090.1912-31.117659.6714-5.6726
3711.20560.45782.2374.4386-1.13558.5625-0.4674-0.25430.7965-0.0916-0.00630.4301-0.45940.40450.47380.3633-0.04650.07370.2090.1140.2564-22.249771.567925.3045
388.4524-0.49350.77254.24850.96885.3946-0.0528-0.89250.15080.2076-0.01270.165-0.65370.00040.06550.50430.07120.07990.37630.07640.376-34.083174.583829.7833
395.53981.85280.01088.07687.26678.82350.0474-0.91910.06650.30450.2141-0.0513-1.06240.3175-0.26151.05590.18490.02660.4203-0.06490.575-43.415683.404325.6422
401.09890.463-0.39779.4998-1.3674.4151-0.0553-0.336-0.1343-0.0766-0.29650.2913-0.3214-0.22620.35180.34140.0729-0.0060.4738-0.02590.4982-51.988280.818122.24
411.70421.3604-0.48126.32881.85669.6958-0.287-0.06530.3329-0.1338-0.01040.7457-0.9533-1.49320.29740.36370.4067-0.13590.5076-0.14360.7702-55.949181.766810.3362
425.55334.05072.60267.89483.151810.7016-0.2266-0.39330.3942-0.0463-0.19360.4914-0.8359-0.77210.42020.25730.2141-0.04690.187-0.0290.5518-58.133572.3976-0.1319
436.69316.4094-2.77929.5072-1.54271.9019-0.10880.21110.096-0.70680.12790.0976-0.24280.0959-0.01910.47940.0469-0.09950.4310.05550.4612-55.748967.485-16.2013
4410.1643-5.4495-3.50432.96461.93091.46260.2534-0.21390.0764-0.1277-0.03080.0386-0.2722-0.3933-0.22250.60530.19860.06370.94820.21370.7567-38.799568.6774-12.7163
4514.46327.41271.457811.20022.05218.50420.2108-0.1284-0.11240.4718-0.11190.1097-0.0954-0.2067-0.09890.2740.13810.00910.13120.01460.3528-56.050162.706-1.8269
4624.50986.4194-1.43596.47221.668.03790.1241.04060.7159-0.3625-0.22970.36290.15980.03250.10570.32510.0795-0.03160.16810.08990.3406-54.856157.0317-8.1799
474.37620.66535.21480.36140.88756.2554-0.1151-0.788-0.0640.25040.13820.1373-0.0906-0.8045-0.02320.6837-0.0020.03870.65830.05380.7332-52.430260.79394.1074
4816.947611.49954.6912.83744.420713.2768-0.53471.21390.0598-0.07730.73190.4742-0.1749-0.0095-0.19720.32070.12630.0650.3337-0.00680.4044-44.89974.503514.62
495.7138-2.6472-0.75912.246-0.24525.8366-0.0411-0.0798-0.09140.37910.094-0.48270.1710.5061-0.05290.3277-0.0163-0.11090.33810.06590.27935.9105-10.8616-29.3698
509.4451.9624-0.845612.5195-10.16128.3408-0.168-0.0965-0.3733-0.7453-0.151-0.59230.70220.23390.3190.8770.144-0.24890.9303-0.18980.984448.3826-10.5714-23.9353
512.55993.65192.47248.21230.05916.58030.143-0.0853-0.13080.4952-0.3387-0.61-0.53150.47190.19570.6319-0.343-0.09840.76070.03380.80843.73842.5047-27.0753
524.5403-1.1531.14579.2043-1.37134.2646-0.0472-0.6331-0.3370.8852-0.0234-0.242-0.01850.69980.07060.6436-0.1764-0.22690.85570.0380.993651.80848.3782-29.5636
535.7409-0.0749-5.1980.46691.957912.8803-0.17870.0249-0.0686-0.16120.0844-0.087-0.15680.31260.09430.5709-0.0355-0.01020.53230.00470.667159.226311.1066-38.4284
543.7978-2.47080.95015.852-1.76552.82450.4030.34480.1473-0.1007-0.5996-1.3887-0.17060.78530.19660.5435-0.19650.17760.7510.01410.924548.510823.5357-45.728
556.23560.6783-3.346912.1622-0.83675.93710.69561.122-0.2258-1.4409-0.3011-0.86710.0271-0.0616-0.39451.07690.07620.22451.0101-0.11620.655436.860827.2532-64.389
562.36181.95280.31461.67680.28180.1308-0.30280.4751-0.0545-0.17130.5442-0.1866-0.21660.0346-0.24141-0.01780.14810.9052-0.02980.79827.2124.9651-62.6208
572.5462-3.78650.665510.83853.02187.29160.03960.03170.1177-0.26010.13730.29110.32680.172-0.17690.4057-0.07250.10280.4564-0.02620.459333.418326.898-49.7993
583.41446.0410.280812.84041.38412.19-0.16810.02340.1782-0.14390.099-0.1197-0.09120.06460.06910.4740.01750.05670.5313-0.07370.444928.664434.6973-51.7642
593.4735-0.90330.65275.5081-1.67490.55920.24820.03220.31060.1499-0.4006-0.1797-0.0330.1350.15240.8541-0.00880.0560.8834-0.11970.813331.145623.0817-45.0659
608.8311-6.9054-6.438233.74967.69055.0521-0.362-0.3360.0960.88330.29990.0260.40380.48140.0620.53530.0688-0.06460.72250.06410.502245.42677.9947-37.9602
614.35860.0801-0.19167.1683-2.61815.38-0.07460.27740.0179-0.2652-0.05260.1781-0.07580.13010.12720.39230.010.00870.3504-0.12680.268616.299832.4622-46.9582
624.97632.27440.61916.16972.80514.6533-0.22060.36480.6764-0.2309-0.09790.9253-0.6819-0.36620.31860.6910.0513-0.11540.5924-0.21170.54228.798323.9556-52.3238
632.9823-3.27360.669222.1978-6.4856.5149-0.2891-0.17310.27960.6006-0.0016-0.27240.2605-0.24740.29070.55440.0164-0.10270.5269-0.03270.45695.982122.7298-65.2086
645.2743-0.1592-0.62676.3659-4.95627.7398-0.0852-0.06990.16410.05680.11070.4919-0.2039-0.1055-0.02550.3724-0.0370.02260.3168-0.1180.36689.159110.0996-57.9399
654.27841.4238-1.96216.722-1.01637.295-0.01230.43790.4673-0.2913-0.04560.3416-0.1213-0.41170.05790.4128-0.0829-0.06550.3361-0.06670.166915.36635.2005-65.4823
669.90741.5066-1.34587.1789-1.56587.4286-0.10970.1216-1.069-0.5828-0.2261-0.8520.21550.08390.33580.3689-0.04560.02860.2807-0.01620.194221.8317-3.3671-64.6614
678.3529-1.69621.53314.5304-1.60434.73-0.30580.0064-0.1193-0.36170.1-0.80020.47010.73180.20580.46320.01550.05120.4131-0.06720.177535.6555-9.4683-55.4294
680.8611.8355-0.977911.7659-3.65291.43580.3105-0.2459-0.0915-1.4972-0.3469-0.28830.09050.28410.03640.76430.0706-0.03990.8097-0.07530.690249.1389-1.2136-47.3327
693.50440.21420.271821.5352-4.60926.68490.0005-0.050.0320.50530.13920.2788-0.14150.0311-0.13970.25140.0242-0.03470.3747-0.00420.241832.3669-9.2165-47.0857
7011.67768.56573.805513.1454-0.21282.5787-0.0787-0.0539-0.68560.47970.1918-0.8873-0.1877-0.0342-0.1130.62010.1244-0.02510.68150.00920.289938.2631-12.6626-41.9696
710.02980.0250.21360.05190.23541.7211-0.0244-0.04550.02720.0579-0.04-0.09780.0779-0.14310.06440.65760.0327-0.05050.63280.02910.677728.8043-2.8111-44.5795
722.05033.9604-4.679530.1104-13.914711.8062-0.10750.15610.313-0.31110.4769-0.53250.1399-0.3309-0.36940.4116-0.1044-0.10730.4625-0.09640.419319.076311.85-56.3656
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA210 - 245
2X-RAY DIFFRACTION2ALLA246 - 259
3X-RAY DIFFRACTION3ALLA260 - 284
4X-RAY DIFFRACTION4ALLA285 - 298
5X-RAY DIFFRACTION5ALLA299 - 366
6X-RAY DIFFRACTION6ALLA367 - 408
7X-RAY DIFFRACTION7ALLA409 - 436
8X-RAY DIFFRACTION8ALLA437 - 449
9X-RAY DIFFRACTION9ALLA450 - 459
10X-RAY DIFFRACTION10ALLA460 - 492
11X-RAY DIFFRACTION11ALLA493 - 531
12X-RAY DIFFRACTION12ALLA532 - 542
13X-RAY DIFFRACTION13ALLB208 - 244
14X-RAY DIFFRACTION14ALLB245 - 291
15X-RAY DIFFRACTION15ALLB292 - 323
16X-RAY DIFFRACTION16ALLB324 - 355
17X-RAY DIFFRACTION17ALLB356 - 374
18X-RAY DIFFRACTION18ALLB375 - 411
19X-RAY DIFFRACTION19ALLB412 - 433
20X-RAY DIFFRACTION20ALLB434 - 457
21X-RAY DIFFRACTION21ALLB460 - 480
22X-RAY DIFFRACTION22ALLB481 - 493
23X-RAY DIFFRACTION23ALLB494 - 536
24X-RAY DIFFRACTION24ALLB537 - 543
25X-RAY DIFFRACTION25ALLC209 - 240
26X-RAY DIFFRACTION26ALLC241 - 253
27X-RAY DIFFRACTION27ALLC254 - 284
28X-RAY DIFFRACTION28ALLC285 - 294
29X-RAY DIFFRACTION29ALLC295 - 317
30X-RAY DIFFRACTION30ALLC318 - 356
31X-RAY DIFFRACTION31ALLC357 - 386
32X-RAY DIFFRACTION32ALLC387 - 434
33X-RAY DIFFRACTION33ALLC435 - 454
34X-RAY DIFFRACTION34ALLC455 - 462
35X-RAY DIFFRACTION35ALLC463 - 531
36X-RAY DIFFRACTION36ALLC532 - 542
37X-RAY DIFFRACTION37ALLD209 - 234
38X-RAY DIFFRACTION38ALLD235 - 284
39X-RAY DIFFRACTION39ALLD285 - 308
40X-RAY DIFFRACTION40ALLD309 - 331
41X-RAY DIFFRACTION41ALLD332 - 375
42X-RAY DIFFRACTION42ALLD376 - 412
43X-RAY DIFFRACTION43ALLD413 - 436
44X-RAY DIFFRACTION44ALLD449 - 459
45X-RAY DIFFRACTION45ALLD460 - 478
46X-RAY DIFFRACTION46ALLD479 - 492
47X-RAY DIFFRACTION47ALLD493 - 533
48X-RAY DIFFRACTION48ALLD534 - 541
49X-RAY DIFFRACTION49ALLE210 - 240
50X-RAY DIFFRACTION50ALLE241 - 258
51X-RAY DIFFRACTION51ALLE259 - 286
52X-RAY DIFFRACTION52ALLE287 - 316
53X-RAY DIFFRACTION53ALLE317 - 336
54X-RAY DIFFRACTION54ALLE337 - 409
55X-RAY DIFFRACTION55ALLE410 - 431
56X-RAY DIFFRACTION56ALLE432 - 455
57X-RAY DIFFRACTION57ALLE457 - 475
58X-RAY DIFFRACTION58ALLE476 - 490
59X-RAY DIFFRACTION59ALLE491 - 535
60X-RAY DIFFRACTION60ALLE536 - 541
61X-RAY DIFFRACTION61ALLF209 - 237
62X-RAY DIFFRACTION62ALLF238 - 282
63X-RAY DIFFRACTION63ALLF283 - 290
64X-RAY DIFFRACTION64ALLF291 - 316
65X-RAY DIFFRACTION65ALLF317 - 351
66X-RAY DIFFRACTION66ALLF352 - 376
67X-RAY DIFFRACTION67ALLF377 - 434
68X-RAY DIFFRACTION68ALLF435 - 454
69X-RAY DIFFRACTION69ALLF460 - 478
70X-RAY DIFFRACTION70ALLF479 - 491
71X-RAY DIFFRACTION71ALLF492 - 535
72X-RAY DIFFRACTION72ALLF536 - 541

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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://pdbjlc1.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