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- PDB-4tvx: Crystal structure of the E. coli CRISPR RNA-guided surveillance c... -

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基本情報

登録情報
データベース: PDB / ID: 4tvx
タイトルCrystal structure of the E. coli CRISPR RNA-guided surveillance complex, Cascade
要素
  • (CRISPR system Cascade subunit ...) x 5
  • Escherichia coli strain ECOR44 cluster 1 CRISPR region
キーワードHydrolase/RNA / CRISPR / RNA / Surveillance / Complex / Hydrolase-RNA complex
機能・相同性
機能・相同性情報


CRISPR-cas system / DNA/RNA hybrid binding / maintenance of CRISPR repeat elements / RNA processing / RNA endonuclease activity / defense response to virus / nucleic acid binding / 加水分解酵素; エステル加水分解酵素 / protein-containing complex / DNA binding ...CRISPR-cas system / DNA/RNA hybrid binding / maintenance of CRISPR repeat elements / RNA processing / RNA endonuclease activity / defense response to virus / nucleic acid binding / 加水分解酵素; エステル加水分解酵素 / protein-containing complex / DNA binding / RNA binding / zinc ion binding
類似検索 - 分子機能
CRISPR-associated protein, CT1975 / CRISPR-associated protein Cse2 / Cse2 superfamily / CT1975-like protein / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein, CasD / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / CRISPR-associated protein Cse3 / CRISPR associated protein ...CRISPR-associated protein, CT1975 / CRISPR-associated protein Cse2 / Cse2 superfamily / CT1975-like protein / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein, CasD / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / CRISPR-associated protein Cse3 / CRISPR associated protein / CRISPR_assoc / CRISPR-associated protein, Cas5 / CRISPR-associated protein (Cas_Cas5) / CRISPR-associated protein Cas5, N-terminal
類似検索 - ドメイン・相同性
: / RNA / RNA (> 10) / CRISPR system Cascade subunit CasB / CRISPR system Cascade subunit CasE / CRISPR system Cascade subunit CasD / CRISPR system Cascade subunit CasC / CRISPR system Cascade subunit CasA
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 解像度: 3.24 Å
データ登録者Jackson, R.N. / Golden, S.M. / Carter, J. / Wiedenheft, B.
資金援助 米国, 4件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20 GM103500 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108888 米国
National Science Foundation (NSF, United States)EPS-110134 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM108436 米国
引用ジャーナル: Science / 年: 2014
タイトル: Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli.
著者: Jackson, R.N. / Golden, S.M. / van Erp, P.B. / Carter, J. / Westra, E.R. / Brouns, S.J. / van der Oost, J. / Terwilliger, T.C. / Read, R.J. / Wiedenheft, B.
履歴
登録2014年6月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年8月13日Provider: repository / タイプ: Initial release
改定 1.12014年8月20日Group: Derived calculations / Other
改定 1.22014年8月27日Group: Database references
改定 1.32014年10月1日Group: Database references
置き換え2014年12月10日ID: 1VY8, 1VY9
改定 1.42014年12月10日Group: Other
改定 1.52017年9月6日Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
カテゴリ: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.62019年11月27日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.72022年3月23日Group: Author supporting evidence / Database references / Refinement description
カテゴリ: database_2 / pdbx_audit_support / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
改定 1.82023年12月27日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond
改定 1.92024年10月23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
W: CRISPR system Cascade subunit CasB
V: CRISPR system Cascade subunit CasB
K: CRISPR system Cascade subunit CasB
J: CRISPR system Cascade subunit CasB
F: CRISPR system Cascade subunit CasC
D: CRISPR system Cascade subunit CasC
E: CRISPR system Cascade subunit CasC
C: CRISPR system Cascade subunit CasC
B: CRISPR system Cascade subunit CasC
G: CRISPR system Cascade subunit CasC
A: CRISPR system Cascade subunit CasE
H: CRISPR system Cascade subunit CasD
R: CRISPR system Cascade subunit CasC
P: CRISPR system Cascade subunit CasC
Q: CRISPR system Cascade subunit CasC
O: CRISPR system Cascade subunit CasC
N: CRISPR system Cascade subunit CasC
S: CRISPR system Cascade subunit CasC
T: CRISPR system Cascade subunit CasD
M: CRISPR system Cascade subunit CasE
L: Escherichia coli strain ECOR44 cluster 1 CRISPR region
X: Escherichia coli strain ECOR44 cluster 1 CRISPR region
U: CRISPR system Cascade subunit CasA
I: CRISPR system Cascade subunit CasA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)804,32526
ポリマ－804,19424
非ポリマー1312
水00
1
W: CRISPR system Cascade subunit CasB
V: CRISPR system Cascade subunit CasB
R: CRISPR system Cascade subunit CasC
P: CRISPR system Cascade subunit CasC
Q: CRISPR system Cascade subunit CasC
O: CRISPR system Cascade subunit CasC
N: CRISPR system Cascade subunit CasC
S: CRISPR system Cascade subunit CasC
T: CRISPR system Cascade subunit CasD
M: CRISPR system Cascade subunit CasE
X: Escherichia coli strain ECOR44 cluster 1 CRISPR region
U: CRISPR system Cascade subunit CasA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)402,16213
ポリマ－402,09712
非ポリマー651
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
K: CRISPR system Cascade subunit CasB
J: CRISPR system Cascade subunit CasB
F: CRISPR system Cascade subunit CasC
D: CRISPR system Cascade subunit CasC
E: CRISPR system Cascade subunit CasC
C: CRISPR system Cascade subunit CasC
B: CRISPR system Cascade subunit CasC
G: CRISPR system Cascade subunit CasC
A: CRISPR system Cascade subunit CasE
H: CRISPR system Cascade subunit CasD
L: Escherichia coli strain ECOR44 cluster 1 CRISPR region
I: CRISPR system Cascade subunit CasA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)402,16213
ポリマ－402,09712
非ポリマー651
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)200.851, 214.541, 217.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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CRISPR system Cascade subunit ... , 5種, 22分子 WVKJFDECBGRPQONSAMHTUI

#1: タンパク質
CRISPR system Cascade subunit CasB


分子量: 19231.049 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K12 / 遺伝子: casB, cse2, ygcK, b2759, JW2729 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P76632
#2: タンパク質
CRISPR system Cascade subunit CasC


分子量: 40071.402 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K12 / 遺伝子: casC, cas4, cse4, ygcJ, b2758, JW2728 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46899
#3: タンパク質 CRISPR system Cascade subunit CasE / CasE endoRNase / crRNA endonuclease


分子量: 22324.002 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K12 / 遺伝子: casE, cas6e, ygcH, b2756, JW2726 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q46897, 加水分解酵素; エステル加水分解酵素
#4: タンパク質 CRISPR system Cascade subunit CasD


分子量: 25239.803 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K12 / 遺伝子: casD, cas5, ygcI, b2757, JW5844 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46898
#6: タンパク質 CRISPR system Cascade subunit CasA / CRISPR type I-E/Ecoli-associated protein CasA/Cse1 / CRISPR-associated protein CasA/Cse1


分子量: 55964.957 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K12 / 遺伝子: casA, cse1, ygcL, b2760, JW2730 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46901

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RNA鎖 / 非ポリマー , 2種, 4分子 LX

#5: RNA鎖 Escherichia coli strain ECOR44 cluster 1 CRISPR region


分子量: 19677.646 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 発現宿主: Escherichia coli (大腸菌) / 参照: GenBank: 50811866
#7: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn

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詳細

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: 2.9 Å3/Da / 溶媒含有率: 60 % / 解説: P212121
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: PEG 8000, sodium chloride, sodium thiocyanate, HEPES
PH範囲: 6.5-8.0 / Temp details: growth occurs at 277-297 K

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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: SSRL / ビームライン: BL12-2 / 波長: 1 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2013年2月4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: 1 Å / 相対比: 1
反射解像度: 3.24→39.614 Å / Num. all: 297628 / Num. obs: 148870 / % possible obs: 98.89 % / 冗長度: 6.8 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 8.5
反射 シェル解像度: 3.24→3.356 Å / 冗長度: 6.9 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.38 / % possible all: 99.9

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解析

ソフトウェア名称: PHENIX / バージョン: (phenix.refine: dev_1760) / 分類: 精密化
精密化解像度: 3.24→39.614 Å / SU ML: 0.39 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 27.62 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2675 2011 1.35 %Random selection
Rwork0.2338 ---
obs0.2342 148795 99.84 %-
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
精密化ステップサイクル: LAST / 解像度: 3.24→39.614 Å
タンパク質核酸リガンド溶媒全体
原子数50698 2564 2 0 53264
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00754544
X-RAY DIFFRACTIONf_angle_d1.23174488
X-RAY DIFFRACTIONf_dihedral_angle_d15.67919862
X-RAY DIFFRACTIONf_chiral_restr0.0478572
X-RAY DIFFRACTIONf_plane_restr0.0069248
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.3210.28361400.318610396X-RAY DIFFRACTION100
3.321-3.41070.32941490.309410363X-RAY DIFFRACTION100
3.4107-3.5110.31771460.295310374X-RAY DIFFRACTION100
3.511-3.62430.33351470.277410386X-RAY DIFFRACTION100
3.6243-3.75370.29741440.263510410X-RAY DIFFRACTION100
3.7537-3.90390.28831350.259610400X-RAY DIFFRACTION100
3.9039-4.08140.28331560.247610421X-RAY DIFFRACTION100
4.0814-4.29630.21761330.23510472X-RAY DIFFRACTION100
4.2963-4.56520.26231400.214810470X-RAY DIFFRACTION100
4.5652-4.9170.21281370.200610475X-RAY DIFFRACTION100
4.917-5.41080.2411460.218710504X-RAY DIFFRACTION100
5.4108-6.19110.30011380.230910559X-RAY DIFFRACTION100
6.1911-7.79050.25261450.234210656X-RAY DIFFRACTION100
7.7905-39.61740.25681550.188210898X-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)
14.4989-0.1819-0.84795.28631.27762.03640.5948-0.4529-1.00770.81010.50540.05851.2636-0.9627-0.80260.940.0126-0.15670.90340.1550.968918.242-23.5862-9.2262
23.08543.258-1.30653.4823-1.3294.4055-0.076-0.9179-0.01891.03640.0210.5585-0.4736-0.54970.11391.12050.0003-0.13761.1652-0.33740.634326.2252-11.5254-6.8969
34.3376-0.31620.7390.9577-1.17114.1541-0.47730.5768-0.4814-0.61760.5181-0.07350.532-0.3547-0.09280.8196-0.1163-0.15490.7837-0.01250.76228.9532-19.7077-17.2563
44.2992-1.450.60582.0237-0.25252.259-0.0744-0.9577-0.24490.57040.32970.11760.2065-0.3239-0.28010.7044-0.0413-0.04790.757-0.02230.5039.7962-16.5618-15.4728
55.93581.22253.87933.6045-1.86076.4279-0.07450.4451-0.1074-0.82050.0692-0.3027-1.04650.96350.03990.7688-0.0830.03060.6984-0.13090.599313.1993-8.5722-25.9317
64.5241-0.7697-2.28071.72220.14585.2643-0.2012-0.5162-0.5123-0.3761-0.22280.64680.6354-0.62570.23950.7388-0.35490.00711.1576-0.06260.680311.468-20.7701-19.2673
78.162-3.0724-2.90116.37411.97966.27250.3788-0.2703-0.5811-0.1651-0.26330.0410.1799-1.0393-0.060.6877-0.0089-0.06040.8022-0.06080.51551.354-15.7507-26.8022
82.55960.01550.1962.49850.59053.1618-0.01010.82070.37250.04520.09260.17380.33611.5158-0.02940.9746-0.0844-0.06921.4369-0.10451.029561.8485-19.9137-31.7787
92.3071-1.36480.29615.8918-0.31424.2824-0.53970.1604-0.76680.1950.97610.58840.87180.5342-0.45220.98270.0046-0.00961.11060.04520.853753.7527-25.4193-23.1054
104.8805-0.84620.4714.58-0.91696.3948-0.0888-0.75721.12030.0337-0.46690.6598-0.0790.53680.46050.9113-0.1231-0.11770.9555-0.15870.786945.0017-15.9271-13.6207
113.509-0.6109-1.08382.00290.25673.0372-0.21250.1136-0.0017-0.3643-0.23680.3624-0.2880.06680.37350.9463-0.0357-0.13240.8568-0.06840.809146.819-20.0637-19.9917
120.06250.1471-0.320.6815-1.20342.3268-0.325-0.8886-0.01961.0524-0.2674-0.7967-0.38190.44640.36250.9711-0.0186-0.13721.15580.141.371371.9504-44.3663-28.6848
134.19790.715-0.94414.40360.70513.84810.01010.95050.0936-0.4949-0.01190.1641-0.82030.08840.00790.7835-0.08240.08640.76510.12440.615574.5847-51.0012-48.4639
145.8658-0.7793-0.55892.84050.38232.6692-0.1118-0.12010.65250.09670.24560.4964-0.63450.1604-0.10850.83140.01250.15350.52870.09160.67470.9324-49.5947-40.1782
155.51970.49781.926.0715-1.19274.67430.10860.9273-0.1566-0.0333-0.0272-0.00830.0187-0.0382-0.0070.56560.0928-0.06370.7649-0.08040.39557.5898-65.5061-40.6016
167.3047-1.21180.71748.5707-0.73687.6308-0.1445-0.13-0.812-0.40620.6030.03480.45190.5489-0.34640.72810.1337-0.11380.36890.01580.527466.5197-62.7631-44.1467
174.85841.2333-0.60063.6981-0.26092.13960.5880.37770.73510.1301-0.1510.0311-0.3926-0.2915-0.45250.61610.13650.07130.57650.15340.673558.2167-57.984-34.718
185.5294-0.3117-0.32513.1913-0.66182.67350.0356-0.487-0.35380.5202-0.2601-0.26410.17091.00390.37290.8124-0.0931-0.08791.0204-0.13361.0178115.0418-62.8323-41.9683
194.6184-0.93510.59182.17760.49013.97020.3024-0.965-0.00650.3605-0.6870.3035-0.6129-0.07350.28380.7506-0.1469-0.05491.1569-0.04831.1326105.733-54.3613-37.9638
204.952-1.19750.54483.81991.06473.2944-0.26371.0947-0.17450.5782-0.02270.3251-0.0431-0.45060.25220.8411-0.2790.1041.0033-0.01410.616397.6399-53.3649-50.2864
215.0653-0.34180.99833.5599-0.16533.26260.1599-0.84440.47740.16740.60470.36320.1295-0.2537-0.52290.659-0.1819-0.00570.8371-0.01140.776995.3823-52.4537-40.6322
221.6373-0.13840.11972.3545-1.05251.632-0.23620.2601-0.4274-0.02050.18660.28490.0814-0.21540.12690.2611-0.05830.06790.4749-0.09930.444564.5741-93.3204-31.4153
231.2969-0.27980.53711.4275-0.03210.7650.25690.3049-1.06810.1567-0.11170.58520.3059-0.6138-0.0210.8898-0.35080.01520.90110.00591.237140.5668-111.6414-27.0638
243.38790.058-0.62182.02540.05063.0582-0.3150.4614-0.54460.95210.88841.46380.1929-1.012-0.73791.3449-0.26620.45970.92780.01781.360542.2571-120.5278-14.0095
253.3271.4165-1.5940.8059-1.38221.6217-0.19450.0721-0.32480.66470.07110.70021.3309-0.28970.27980.8433-0.23440.26820.4976-0.01990.885253.9969-109.7004-18.1344
261.6568-0.3484-0.17391.6666-0.74433.5387-0.06110.2566-0.2942-0.14740.07590.16760.2633-0.24890.04320.2178-0.0850.04960.4004-0.14060.446864.3924-94.4392-34.5916
273.4974-2.08282.64562.2934-3.54375.6280.22730.11890.2063-0.2556-0.189-0.41161.0777-0.07710.0180.49130.07890.00270.3327-0.13250.549769.7129-96.8042-36.8624
283.10311.8674-1.15536.0022-2.10835.7647-0.1575-0.1049-0.06980.5011-0.0913-0.7443-0.40250.45860.32580.3396-0.0095-0.13520.5185-0.03810.326378.4853-87.223-25.1308
292.2992-1.02824.50143.0032-4.90142.0871-0.53610.07150.0186-0.152-0.7715-1.20530.07061.91731.16530.43390.0660.04970.51190.13920.668784.3946-90.8579-23.3257
303.3613-0.8371.0843.62991.35538.0039-0.25120.3595-0.3969-0.0278-0.1626-1.03871.28641.93810.1410.56590.26980.12770.5355-0.02820.710483.8534-105.5477-28.079
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1175.3781.3746-1.90272.1162.39245.4272-0.40250.73970.9251-1.89390.43070.7117-0.3688-0.4372-0.26530.7620.0956-0.02680.65250.07650.5061-12.417-22.5394-81.2648
1183.0439-2.8266-0.17686.1544-1.36510.9884-0.1853-0.1489-0.36870.36630.1280.3364-0.02010.04710.11770.343-0.13770.02830.4405-0.06880.3326-1.7122-38.5189-61.5708
1193.76774.5327-0.80445.2506-0.78280.16170.01210.6887-0.4311-0.35050.2247-1.00230.1934-0.2367-0.25451.06570.08940.23170.5948-0.17120.83027.5211-57.6953-72.7486
1207.2702-2.560.10673.0932-1.24550.8955-0.18770.49330.09140.3220.0296-0.53220.3111-0.12920.14610.6185-0.05780.13140.3088-0.01720.558.2155-40.0322-68.3896
1210.58280.13040.04450.62270.43820.77230.0519-0.5004-0.76270.5262-0.0602-0.05750.73590.00210.02181.03160.01940.01760.62840.13930.85671.2965-57.5767-55.2224
1220.6927-0.9356-0.34371.0238-0.08351.39330.4729-0.0377-0.2366-0.1604-0.31070.44970.32650.3826-0.10960.8174-0.1221-0.01090.43110.01140.6992-9.9607-50.2504-65.6045
1233.1768-0.2571-0.6833.0274-0.18173.03620.16010.48540.1166-0.5660.03890.43810.4432-0.8259-0.24950.7938-0.0082-0.11641.03230.16880.823676.3239-1.5132-43.6404
1241.9013-0.1129-0.34740.95680.78392.0408-0.18420.4017-0.07550.15830.114-0.37020.32410.15850.07570.7877-0.0128-0.14780.80890.06760.745189.3415-7.7531-34.0355
1254.7399-0.8274-1.02661.50660.13623.14980.2764-0.0355-0.55660.86570.06-0.80820.28930.2167-0.30970.83770.101-0.17250.73790.01550.763393.3739-3.9739-23.2352
1262.98390.6694-0.34011.5655-1.54253.12290.13510.32710.0013-0.45631.265-0.14190.3682-0.2129-0.65091.1268-0.29690.04540.9429-0.17010.950379.4611-16.7236-35.5664
1270.8142-1.8757-1.89438.2912-0.59842.06270.0908-0.46850.18841.22130.2409-0.28820.38380.787-0.08620.6881-0.0948-0.16481.11160.03910.621792.07962.8682-25.0771
1282.3690.51430.00594.99430.70982.5375-0.03960.63120.21690.04250.3563-0.4310.29130.2085-0.13420.67060.0465-0.08310.8923-0.02320.700890.16431.2843-34.8279
1291.80820.4565-0.63082.48841.252.670.0089-0.3213-0.19360.40130.12910.37080.2343-0.0952-0.06070.44180.04480.05450.36240.05910.393757.3928-86.56256.0606
1301.7438-0.063-0.62080.2793-0.76321.7660.07690.57090.36260.05470.17040.3403-0.1669-0.4811-0.10230.4335-0.01160.03460.5072-0.08580.43968.3125-70.1563-55.2096
1310.74191.3059-1.3954.1005-0.55523.9511-0.0219-0.80240.33570.12950.2910.3104-0.94650.597-0.38220.9092-0.29050.21230.8295-0.05861.0984122.007-45.2499-60.6602
1321.3841.0619-0.83791.47190.19691.1893-0.5066-0.54660.76250.47270.3158-0.3409-1.14531.02360.0881.0247-0.4956-0.1151.3053-0.220.9904138.693-64.8926-43.4707
1334.29190.7245-0.06810.1965-0.39171.09330.6349-0.5299-0.20560.3774-0.0839-1.46830.13590.4312-0.37661.4224-0.324-0.57912.121-0.12691.9533156.8382-68.705-41.7025
1344.32530.8676-1.43836.3175-1.64314.2680.1724-0.0414-0.1490.505-0.3406-0.8223-0.12431.22240.41850.8512-0.3666-0.19131.8367-0.30081.1731145.9053-73.6565-46.9642
1350.35590.91390.96831.5109-0.29340.528-0.0806-0.06990.0195-0.3719-0.02160.2328-0.0213-0.08080.05060.2883-0.0050.05180.2753-0.04490.393-2.6912-19.3266-66.062
1360.7994-0.55020.94160.3744-0.18191.5086-0.2256-0.62860.24280.0570.1661-0.1509-0.1106-0.35060.16540.5893-0.0943-0.07610.5688-0.09480.728835.08121.1203-10.2142
1370.3728-0.04060.14351.0631-0.45720.2557-0.486-1.0861-0.16670.72970.9631-0.1310.4297-0.6137-0.41511.60080.1534-0.15881.03710.14030.915485.7698-21.8272-23.9641
1382.98010.8334-1.36923.22390.44665.07960.0312-0.2114-1.01640.18550.3026-1.20671.40451.5003-0.08681.22620.2997-0.19451.2142-0.20811.237697.8265-17.413-40.4868
1392.25820.57520.70081.0223-0.3620.8701-0.17230.0232-0.7573-0.1391-0.01230.2960.5729-0.47420.06690.8878-0.37290.04970.8075-0.13340.9233-34.004-56.8816-66.1561
1402.40441.2492-0.58781.9023-0.74862.886-0.02640.04110.2622-0.1354-0.14630.5504-0.1717-0.78770.14560.53840.0048-0.05480.5748-0.12060.6832-36.1686-38.1091-67.2492
1412.96951.0211.14730.74091.00091.57620.4115-0.7695-0.17260.3558-0.44710.3013-0.0810.0096-0.04620.7505-0.15450.0270.7048-0.11550.6205-28.3399-44.0181-51.8397
1424.32342.2520.61483.86690.14541.68890.0528-0.2467-0.34990.3263-0.1332-0.12240.1906-0.50920.10920.5589-0.14460.07550.63290.02060.4596-11.2169-28.1454-38.3522
1433.1225-1.62270.53762.2404-1.48311.56110.8393-1.9313-1.92111.46940.7061-0.1499-0.0614-1.835-0.31660.54920.8851.77951.95930.2297-0.651829.6782-76.079425.5777
1440.7709-1.9528-0.65332.5521-0.121.3888-0.071-0.3093-0.35020.40870.29310.5922-0.2211-0.9724-0.17170.91870.16210.29671.70450.2330.800522.2054-80.16518.2973
1452.6448-0.8497-1.3320.8332-0.47213.116-0.1327-0.52730.17090.44180.38810.2749-0.6164-0.8603-0.19940.67960.29320.17810.94890.02430.660436.9723-64.8052-6.0278
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'W' and (resid 4 through 16 )
2X-RAY DIFFRACTION2chain 'W' and (resid 17 through 26 )
3X-RAY DIFFRACTION3chain 'W' and (resid 27 through 54 )
4X-RAY DIFFRACTION4chain 'W' and (resid 55 through 98 )
5X-RAY DIFFRACTION5chain 'W' and (resid 99 through 124 )
6X-RAY DIFFRACTION6chain 'W' and (resid 125 through 141 )
7X-RAY DIFFRACTION7chain 'W' and (resid 142 through 160 )
8X-RAY DIFFRACTION8chain 'V' and (resid 4 through 54 )
9X-RAY DIFFRACTION9chain 'V' and (resid 55 through 86 )
10X-RAY DIFFRACTION10chain 'V' and (resid 87 through 109 )
11X-RAY DIFFRACTION11chain 'V' and (resid 110 through 158 )
12X-RAY DIFFRACTION12chain 'K' and (resid 0 through 8 )
13X-RAY DIFFRACTION13chain 'K' and (resid 9 through 37 )
14X-RAY DIFFRACTION14chain 'K' and (resid 38 through 86 )
15X-RAY DIFFRACTION15chain 'K' and (resid 87 through 109 )
16X-RAY DIFFRACTION16chain 'K' and (resid 110 through 124 )
17X-RAY DIFFRACTION17chain 'K' and (resid 125 through 160 )
18X-RAY DIFFRACTION18chain 'J' and (resid 4 through 51 )
19X-RAY DIFFRACTION19chain 'J' and (resid 52 through 86 )
20X-RAY DIFFRACTION20chain 'J' and (resid 87 through 124 )
21X-RAY DIFFRACTION21chain 'J' and (resid 125 through 160 )
22X-RAY DIFFRACTION22chain 'F' and (resid 2 through 57 )
23X-RAY DIFFRACTION23chain 'F' and (resid 58 through 115 )
24X-RAY DIFFRACTION24chain 'F' and (resid 116 through 145 )
25X-RAY DIFFRACTION25chain 'F' and (resid 146 through 184 )
26X-RAY DIFFRACTION26chain 'F' and (resid 185 through 260 )
27X-RAY DIFFRACTION27chain 'F' and (resid 261 through 284 )
28X-RAY DIFFRACTION28chain 'F' and (resid 285 through 304 )
29X-RAY DIFFRACTION29chain 'F' and (resid 305 through 323 )
30X-RAY DIFFRACTION30chain 'F' and (resid 324 through 363 )
31X-RAY DIFFRACTION31chain 'D' and (resid 2 through 57 )
32X-RAY DIFFRACTION32chain 'D' and (resid 58 through 146 )
33X-RAY DIFFRACTION33chain 'D' and (resid 147 through 260 )
34X-RAY DIFFRACTION34chain 'D' and (resid 261 through 304 )
35X-RAY DIFFRACTION35chain 'D' and (resid 305 through 323 )
36X-RAY DIFFRACTION36chain 'D' and (resid 324 through 362 )
37X-RAY DIFFRACTION37chain 'E' and (resid 2 through 57 )
38X-RAY DIFFRACTION38chain 'E' and (resid 58 through 115 )
39X-RAY DIFFRACTION39chain 'E' and (resid 116 through 146 )
40X-RAY DIFFRACTION40chain 'E' and (resid 147 through 260 )
41X-RAY DIFFRACTION41chain 'E' and (resid 261 through 284 )
42X-RAY DIFFRACTION42chain 'E' and (resid 285 through 303 )
43X-RAY DIFFRACTION43chain 'E' and (resid 304 through 323 )
44X-RAY DIFFRACTION44chain 'E' and (resid 324 through 363 )
45X-RAY DIFFRACTION45chain 'C' and (resid 2 through 57 )
46X-RAY DIFFRACTION46chain 'C' and (resid 58 through 144 )
47X-RAY DIFFRACTION47chain 'C' and (resid 145 through 362 )
48X-RAY DIFFRACTION48chain 'B' and (resid 2 through 27 )
49X-RAY DIFFRACTION49chain 'B' and (resid 28 through 57 )
50X-RAY DIFFRACTION50chain 'B' and (resid 58 through 174 )
51X-RAY DIFFRACTION51chain 'B' and (resid 175 through 362 )
52X-RAY DIFFRACTION52chain 'G' and (resid 2 through 57 )
53X-RAY DIFFRACTION53chain 'G' and (resid 58 through 79 )
54X-RAY DIFFRACTION54chain 'G' and (resid 80 through 173 )
55X-RAY DIFFRACTION55chain 'G' and (resid 174 through 212 )
56X-RAY DIFFRACTION56chain 'G' and (resid 213 through 304 )
57X-RAY DIFFRACTION57chain 'G' and (resid 305 through 322 )
58X-RAY DIFFRACTION58chain 'G' and (resid 323 through 362 )
59X-RAY DIFFRACTION59chain 'A' and (resid 1 through 118 )
60X-RAY DIFFRACTION60chain 'A' and (resid 119 through 160 )
61X-RAY DIFFRACTION61chain 'A' and (resid 161 through 171 )
62X-RAY DIFFRACTION62chain 'A' and (resid 172 through 199 )
63X-RAY DIFFRACTION63chain 'H' and (resid 1 through 68 )
64X-RAY DIFFRACTION64chain 'H' and (resid 69 through 88 )
65X-RAY DIFFRACTION65chain 'H' and (resid 89 through 103 )
66X-RAY DIFFRACTION66chain 'H' and (resid 104 through 183 )
67X-RAY DIFFRACTION67chain 'H' and (resid 184 through 219 )
68X-RAY DIFFRACTION68chain 'R' and (resid 2 through 27 )
69X-RAY DIFFRACTION69chain 'R' and (resid 28 through 57 )
70X-RAY DIFFRACTION70chain 'R' and (resid 58 through 145 )
71X-RAY DIFFRACTION71chain 'R' and (resid 146 through 184 )
72X-RAY DIFFRACTION72chain 'R' and (resid 185 through 260 )
73X-RAY DIFFRACTION73chain 'R' and (resid 261 through 284 )
74X-RAY DIFFRACTION74chain 'R' and (resid 285 through 303 )
75X-RAY DIFFRACTION75chain 'R' and (resid 304 through 322 )
76X-RAY DIFFRACTION76chain 'R' and (resid 323 through 363 )
77X-RAY DIFFRACTION77chain 'P' and (resid 2 through 57 )
78X-RAY DIFFRACTION78chain 'P' and (resid 58 through 145 )
79X-RAY DIFFRACTION79chain 'P' and (resid 146 through 260 )
80X-RAY DIFFRACTION80chain 'P' and (resid 261 through 284 )
81X-RAY DIFFRACTION81chain 'P' and (resid 285 through 362 )
82X-RAY DIFFRACTION82chain 'Q' and (resid 2 through 57 )
83X-RAY DIFFRACTION83chain 'Q' and (resid 58 through 79 )
84X-RAY DIFFRACTION84chain 'Q' and (resid 80 through 146 )
85X-RAY DIFFRACTION85chain 'Q' and (resid 147 through 195 )
86X-RAY DIFFRACTION86chain 'Q' and (resid 196 through 260 )
87X-RAY DIFFRACTION87chain 'Q' and (resid 261 through 284 )
88X-RAY DIFFRACTION88chain 'Q' and (resid 285 through 304 )
89X-RAY DIFFRACTION89chain 'Q' and (resid 305 through 322 )
90X-RAY DIFFRACTION90chain 'Q' and (resid 323 through 362 )
91X-RAY DIFFRACTION91chain 'O' and (resid 2 through 57 )
92X-RAY DIFFRACTION92chain 'O' and (resid 58 through 145 )
93X-RAY DIFFRACTION93chain 'O' and (resid 146 through 260 )
94X-RAY DIFFRACTION94chain 'O' and (resid 261 through 284 )
95X-RAY DIFFRACTION95chain 'O' and (resid 285 through 323 )
96X-RAY DIFFRACTION96chain 'O' and (resid 324 through 362 )
97X-RAY DIFFRACTION97chain 'N' and (resid 2 through 57 )
98X-RAY DIFFRACTION98chain 'N' and (resid 58 through 184 )
99X-RAY DIFFRACTION99chain 'N' and (resid 185 through 206 )
100X-RAY DIFFRACTION100chain 'N' and (resid 207 through 362 )
101X-RAY DIFFRACTION101chain 'S' and (resid 2 through 27 )
102X-RAY DIFFRACTION102chain 'S' and (resid 28 through 57 )
103X-RAY DIFFRACTION103chain 'S' and (resid 58 through 84 )
104X-RAY DIFFRACTION104chain 'S' and (resid 85 through 112 )
105X-RAY DIFFRACTION105chain 'S' and (resid 113 through 173 )
106X-RAY DIFFRACTION106chain 'S' and (resid 174 through 222 )
107X-RAY DIFFRACTION107chain 'S' and (resid 223 through 260 )
108X-RAY DIFFRACTION108chain 'S' and (resid 261 through 284 )
109X-RAY DIFFRACTION109chain 'S' and (resid 285 through 304 )
110X-RAY DIFFRACTION110chain 'S' and (resid 305 through 322 )
111X-RAY DIFFRACTION111chain 'S' and (resid 323 through 362 )
112X-RAY DIFFRACTION112chain 'T' and (resid 1 through 19 )
113X-RAY DIFFRACTION113chain 'T' and (resid 20 through 32 )
114X-RAY DIFFRACTION114chain 'T' and (resid 33 through 50 )
115X-RAY DIFFRACTION115chain 'T' and (resid 51 through 68 )
116X-RAY DIFFRACTION116chain 'T' and (resid 69 through 89 )
117X-RAY DIFFRACTION117chain 'T' and (resid 90 through 102 )
118X-RAY DIFFRACTION118chain 'T' and (resid 103 through 122 )
119X-RAY DIFFRACTION119chain 'T' and (resid 123 through 138 )
120X-RAY DIFFRACTION120chain 'T' and (resid 139 through 157 )
121X-RAY DIFFRACTION121chain 'T' and (resid 158 through 196 )
122X-RAY DIFFRACTION122chain 'T' and (resid 197 through 219 )
123X-RAY DIFFRACTION123chain 'M' and (resid 1 through 65 )
124X-RAY DIFFRACTION124chain 'M' and (resid 66 through 118 )
125X-RAY DIFFRACTION125chain 'M' and (resid 119 through 143 )
126X-RAY DIFFRACTION126chain 'M' and (resid 144 through 160 )
127X-RAY DIFFRACTION127chain 'M' and (resid 161 through 171 )
128X-RAY DIFFRACTION128chain 'M' and (resid 172 through 199 )
129X-RAY DIFFRACTION129chain 'L' and (resid 1 through 10 )
130X-RAY DIFFRACTION130chain 'L' and (resid 11 through 35 )
131X-RAY DIFFRACTION131chain 'L' and (resid 36 through 40 )
132X-RAY DIFFRACTION132chain 'L' and (resid 41 through 50 )
133X-RAY DIFFRACTION133chain 'L' and (resid 51 through 55 )
134X-RAY DIFFRACTION134chain 'L' and (resid 56 through 60 )
135X-RAY DIFFRACTION135chain 'X' and (resid 1 through 15 )
136X-RAY DIFFRACTION136chain 'X' and (resid 16 through 40 )
137X-RAY DIFFRACTION137chain 'X' and (resid 41 through 45 )
138X-RAY DIFFRACTION138chain 'X' and (resid 46 through 60 )
139X-RAY DIFFRACTION139chain 'U' and (resid 3 through 84 )
140X-RAY DIFFRACTION140chain 'U' and (resid 85 through 328 )
141X-RAY DIFFRACTION141chain 'U' and (resid 329 through 375 )
142X-RAY DIFFRACTION142chain 'U' and (resid 376 through 496 )
143X-RAY DIFFRACTION143chain 'I' and (resid 3 through 153 )
144X-RAY DIFFRACTION144chain 'I' and (resid 154 through 278 )
145X-RAY DIFFRACTION145chain 'I' and (resid 279 through 496 )

+
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

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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