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- PDB-6b2o: LarE, a sulfur transferase involved in synthesis of the cofactor ... -

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基本情報

登録情報
データベース: PDB / ID: 6b2o
タイトルLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, C176A variant
要素ATP-utilizing enzyme of the PP-loopsuperfamily
キーワードTRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / hexamer / trimer / PP-loop / ATP / magnesium / ATP pyrophophatase domain / lactate / lactate racemization / lactate racemase / cysteine to alanine
機能・相同性
機能・相同性情報


pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase / NAD+ synthase (glutamine-hydrolyzing) activity / sulfurtransferase activity / lyase activity / ATP binding
類似検索 - 分子機能
Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase LarE / NAD/GMP synthase / NAD synthase / Rossmann-like alpha/beta/alpha sandwich fold
類似検索 - ドメイン・相同性
PHOSPHATE ION / Uncharacterized protein / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase
類似検索 - 構成要素
生物種Lactobacillus plantarum (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.35 Å
データ登録者Fellner, M. / Hausinger, R.P. / Hu, J.
資金援助 米国, 1件
組織認可番号国
National Science Foundation (NSF, United States)CHE-1516126 米国
引用ジャーナル: Biochemistry / 年: 2018
タイトル: Analysis of the Active Site Cysteine Residue of the Sacrificial Sulfur Insertase LarE from Lactobacillus plantarum.
著者: Fellner, M. / Rankin, J.A. / Desguin, B. / Hu, J. / Hausinger, R.P.
履歴
登録2017年9月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年9月5日Provider: repository / タイプ: Initial release
改定 1.12018年9月12日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22018年10月10日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32019年2月20日Group: Author supporting evidence / Data collection / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42019年11月27日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52023年10月4日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ATP-utilizing enzyme of the PP-loopsuperfamily
B: ATP-utilizing enzyme of the PP-loopsuperfamily
C: ATP-utilizing enzyme of the PP-loopsuperfamily
D: ATP-utilizing enzyme of the PP-loopsuperfamily
E: ATP-utilizing enzyme of the PP-loopsuperfamily
F: ATP-utilizing enzyme of the PP-loopsuperfamily
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)191,17017
ポリマ－190,1206
非ポリマー1,05011
水8,881493
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-65 kcal/mol
Surface area63850 Å2
手法PISA
単位格子
Length a, b, c (Å)108.660, 108.660, 328.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDモデル要素
11B-495-

HOH

21B-529-

HOH

31E-445-

HOH

41E-451-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 5 through 6 or (resid 7...
21(chain B and (resid 5 through 6 or (resid 7...
31(chain C and (resid 5 through 6 or (resid 7...
41(chain D and (resid 5 through 43 or (resid 44...
51(chain E and (resid 5 through 6 or (resid 7...
61(chain F and (resid 5 through 6 or (resid 7...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATHRTHR(chain A and (resid 5 through 6 or (resid 7...AA5 - 65 - 6
12LYSLYSALAALA(chain A and (resid 5 through 6 or (resid 7...AA7 - 97 - 9
13ALAALAALAALA(chain A and (resid 5 through 6 or (resid 7...AA2 - 2762 - 276
14ALAALAALAALA(chain A and (resid 5 through 6 or (resid 7...AA2 - 2762 - 276
15ALAALAALAALA(chain A and (resid 5 through 6 or (resid 7...AA2 - 2762 - 276
16ALAALAALAALA(chain A and (resid 5 through 6 or (resid 7...AA2 - 2762 - 276
21ALAALATHRTHR(chain B and (resid 5 through 6 or (resid 7...BB5 - 65 - 6
22LYSLYSALAALA(chain B and (resid 5 through 6 or (resid 7...BB7 - 97 - 9
23ALAALAARGARG(chain B and (resid 5 through 6 or (resid 7...BB2 - 2592 - 259
24ALAALAARGARG(chain B and (resid 5 through 6 or (resid 7...BB2 - 2592 - 259
25ALAALAARGARG(chain B and (resid 5 through 6 or (resid 7...BB2 - 2592 - 259
26ALAALAARGARG(chain B and (resid 5 through 6 or (resid 7...BB2 - 2592 - 259
31ALAALATHRTHR(chain C and (resid 5 through 6 or (resid 7...CC5 - 65 - 6
32LYSLYSALAALA(chain C and (resid 5 through 6 or (resid 7...CC7 - 97 - 9
33ALAALAARGARG(chain C and (resid 5 through 6 or (resid 7...CC2 - 2592 - 259
34ALAALAARGARG(chain C and (resid 5 through 6 or (resid 7...CC2 - 2592 - 259
35ALAALAARGARG(chain C and (resid 5 through 6 or (resid 7...CC2 - 2592 - 259
36ALAALAARGARG(chain C and (resid 5 through 6 or (resid 7...CC2 - 2592 - 259
41ALAALAGLYGLY(chain D and (resid 5 through 43 or (resid 44...DD5 - 435 - 43
42ARGARGARGARG(chain D and (resid 5 through 43 or (resid 44...DD4444
43ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
44ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
45ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
46ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
47ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
48ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
49ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
51ALAALATHRTHR(chain E and (resid 5 through 6 or (resid 7...EE5 - 65 - 6
52LYSLYSALAALA(chain E and (resid 5 through 6 or (resid 7...EE7 - 97 - 9
53ALAALATRPTRP(chain E and (resid 5 through 6 or (resid 7...EE2 - 2792 - 279
54ALAALATRPTRP(chain E and (resid 5 through 6 or (resid 7...EE2 - 2792 - 279
55ALAALATRPTRP(chain E and (resid 5 through 6 or (resid 7...EE2 - 2792 - 279
56ALAALATRPTRP(chain E and (resid 5 through 6 or (resid 7...EE2 - 2792 - 279
61ALAALATHRTHR(chain F and (resid 5 through 6 or (resid 7...FF5 - 65 - 6
62LYSLYSALAALA(chain F and (resid 5 through 6 or (resid 7...FF7 - 97 - 9
63ALAALASERSER(chain F and (resid 5 through 6 or (resid 7...FF2 - 2602 - 260
64ALAALASERSER(chain F and (resid 5 through 6 or (resid 7...FF2 - 2602 - 260
65ALAALASERSER(chain F and (resid 5 through 6 or (resid 7...FF2 - 2602 - 260
66ALAALASERSER(chain F and (resid 5 through 6 or (resid 7...FF2 - 2602 - 260

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要素

#1: タンパク質
ATP-utilizing enzyme of the PP-loopsuperfamily / Lactate racemization operon protein LarE / PP-loop superfamily ATP-binding protein / TIGR00268 family protein


分子量: 31686.703 Da / 分子数: 6 / 変異: C176A / 由来タイプ: 組換発現
由来: (組換発現) Lactobacillus plantarum (バクテリア)
遺伝子: A8P51_04975, AVR82_02840, BIZ32_00440, IV39_GL000116, LPJSA22_00116, Nizo1839_0768, Nizo2891_3302, SRCM101060_01452
プラスミド: pGIR076-C176A / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Arctic express DE3 / 参照: UniProt: A0A0G9FES3, UniProt: F9UST4*PLUS
#2: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 6 / 由来タイプ: 合成 / 式: PO4
#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 5 / 由来タイプ: 合成 / 式: SO4
#4: 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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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: 2.55 Å3/Da / 溶媒含有率: 51.79 % / Mosaicity: 0.17 °
結晶化温度: 294.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 5 ul 8 mg/ml LarE-C176A (100 mM Tris-HCl pH 7.5, 300 mM NaCl) were mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 ...詳細: 5 ul 8 mg/ml LarE-C176A (100 mM Tris-HCl pH 7.5, 300 mM NaCl) were mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 100 mM ammonium sulfate.

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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: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2016年11月25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: 2.35→48.67 Å / Num. obs: 82741 / % possible obs: 99.5 % / 冗長度: 11.3 % / Biso Wilson estimate: 41.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.034 / Rrim(I) all: 0.114 / Net I/σ(I): 18.9 / Num. measured all: 932078 / Scaling rejects: 2
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.35-2.3911.21.1343450.7020.3471.18397.3
12.19-48.678.10.0237080.9990.0080.02597.4

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation7.61 Å48.67 Å
Translation7.61 Å48.67 Å

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解析

ソフトウェア
名称バージョン分類
Aimless0.5.28データスケーリング
PHASER2.7.16位相決定
PHENIX1.12-2829精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 5UDQ

5udq


解像度: 2.35→48.67 Å / SU ML: 0.33 / 交差検証法: FREE R-VALUE / σ(F): 1.91 / 位相誤差: 24.94
Rfactor反射数%反射
Rfree0.2436 7813 5 %
Rwork0.1872 --
obs0.19 78172 99.41 %
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: 160.55 Å2 / Biso mean: 56.3395 Å2 / Biso min: 22.03 Å2
精密化ステップサイクル: final / 解像度: 2.35→48.67 Å
タンパク質核酸リガンド溶媒全体
原子数11365 0 55 493 11913
Biso mean--52.18 48.37 -
残基数----1500
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00711585
X-RAY DIFFRACTIONf_angle_d0.92215729
X-RAY DIFFRACTIONf_chiral_restr0.0591843
X-RAY DIFFRACTIONf_plane_restr0.0062035
X-RAY DIFFRACTIONf_dihedral_angle_d4.1026859
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A6043X-RAY DIFFRACTION10.225TORSIONAL
12B6043X-RAY DIFFRACTION10.225TORSIONAL
13C6043X-RAY DIFFRACTION10.225TORSIONAL
14D6043X-RAY DIFFRACTION10.225TORSIONAL
15E6043X-RAY DIFFRACTION10.225TORSIONAL
16F6043X-RAY DIFFRACTION10.225TORSIONAL
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 (%)
2.3466-2.37330.3362220.29244781500395
2.3733-2.40120.3442450.26784989523499
2.4012-2.43050.30312670.2644903517099
2.4305-2.46130.33952870.26644914520199
2.4613-2.49370.33662750.28264920519599
2.4937-2.52780.33752540.26835014526899
2.5278-2.56390.33042470.25284895514299
2.5639-2.60220.31522600.24854986524699
2.6022-2.64290.30022560.23614971522799
2.6429-2.68620.31782610.23164894515599
2.6862-2.73250.27072320.234978521099
2.7325-2.78220.30932630.22654966522999
2.7822-2.83570.25542600.223549665226100
2.8357-2.89360.27692630.214949355198100
2.8936-2.95650.28222820.220549555237100
2.9565-3.02520.32512650.231949825247100
3.0252-3.10090.30412870.225549035190100
3.1009-3.18470.30472290.220249915220100
3.1847-3.27840.26472670.204549575224100
3.2784-3.38420.27042550.200649785233100
3.3842-3.50510.25832470.184349775224100
3.5051-3.64540.21782700.176349435213100
3.6454-3.81130.22942820.16549245206100
3.8113-4.01210.18872470.152350035250100
4.0121-4.26330.20832460.147950035249100
4.2633-4.59230.18282410.13549745215100
4.5923-5.0540.20472780.135649645242100
5.054-5.78430.17832750.149249605235100
5.7843-7.28370.20612970.169749525249100
7.2837-48.6840.20212530.1664952520599
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)
16.70454.87590.91357.61550.30452.9041-0.05070.21440.157-0.08570.18630.1458-0.0140.2431-0.15080.34130.0693-0.0440.40340.00380.244618.97830.2741-14.3094
22.8698-3.01581.2232.2764-5.3953.92080.41790.4655-0.2121-1.8221-0.7358-0.34351.23681.09680.24150.70390.2519-0.02570.72020.02440.398518.1865-16.221-25.6837
39.9189-1.93513.72286.9883-2.59067.95180.26821.2152-0.5494-0.43050.0771-0.64580.64342.1854-0.35650.3699-0.0080.01060.7293-0.07980.439229.8318-0.3801-15.3048
40.4339-0.4086-0.73564.3496-0.57410.05320.04430.11-0.0639-0.6333-0.1360.2494-0.1211-0.1270.08870.5890.1643-0.13640.46080.00870.367917.1303-21.5325-8.6772
55.0592-1.93870.16332.14280.01632.37350.18550.32140.4223-0.2454-0.1176-0.1714-0.24090.0465-0.06310.44430.0697-0.03540.29530.02860.365724.3859-32.6371-1.6398
61.18270.3371-0.2361.8915-2.58234.47270.00010.00980.20770.1459-0.1542-0.0168-0.34450.20460.13420.25470.014-0.06770.1979-0.04850.32858.92381.976423.032
76.26827.5639-4.0639.349-6.29696.1786-0.18930.35110.52630.08120.39620.7354-0.1103-0.4962-0.15840.30640.0832-0.10130.3275-0.06010.34-1.49320.067129.2981
83.0056-2.8532-5.6055.66863.22867.6359-0.35020.456-0.63950.1584-0.16470.50830.731-0.70760.5040.3187-0.0152-0.07040.37070.01330.38494.86560.691112.1305
9-0.3981-0.22740.33151.5793-0.9981.22770.0310.07960.0968-0.3643-0.06320.06110.2231-0.12520.04120.3522-0.0061-0.04830.2819-0.01420.296712.869-15.153629.1874
103.1971-0.83350.08285.99832.56062.6669-0.0527-0.0881-0.0325-0.171-0.0013-0.0378-0.06570.11340.11250.25820.0041-0.00720.25930.00840.214318.3889-27.038627.5268
117.41652.1137-2.42488.76123.05539.018-0.48430.15760.0601-0.0971-0.2988-0.1858-0.0235-0.24760.7590.27030.0576-0.05960.1614-0.01860.35613.4167-29.590228.9395
125.7463-4.0481-0.2646.1179-0.76272.16520.1386-0.1609-0.2318-0.09370.11620.1637-0.0620.0835-0.24230.3163-0.0576-0.06080.24950.0240.367444.16644.752310.9521
138.4273-6.32446.93132.07011.67061.9346-0.23-0.61880.41550.61680.0696-0.9896-0.4632-0.57770.3790.3667-0.03450.01560.441-0.10370.520655.02714.258314.965
146.2053-3.3265-2.35635.10832.77863.6657-0.5675-1.4931-0.15320.49050.3801-0.26240.11850.46430.15740.4261-0.05070.01090.51980.04920.426644.135910.510720.9983
152.19820.76072.58360.49890.26151.7263-0.1324-0.6492-0.4205-0.18820.39011.41730.5085-0.4104-0.23950.4958-0.0203-0.00860.5420.29050.859531.40351.714215.0456
163.04670.99920.40853.38090.871.7579-0.02-0.07660.1901-0.11130.0536-0.2621-0.16460.0132-0.04080.39370.07190.01240.27580.03820.308645.9637-23.801513.9402
178.40222.5108-2.05543.7839-4.07174.25970.0037-0.05140.8893-0.01250.20190.327-0.00180.0801-0.29610.34320.0499-0.02970.2606-0.02450.261146.0876-28.398318.3048
186.6355-4.95741.20774.8090.71492.5224-0.8227-1.29290.35170.91521.4325-0.98160.11220.3457-0.5351.64750.18510.46850.6887-0.00021.17720.7603-77.834835.2743
190.60751.52280.74424.2912.20251.21070.1996-0.5434-1.0127-1.1569-1.00250.36211.3563-0.60390.64451.3263-0.04410.37730.36160.07791.12528.0404-70.481131.9963
202.9266-1.7555-0.41795.63491.58651.10410.00440.2697-0.8245-2.129-0.60780.25191.05310.15010.51152.0728-0.10220.20050.54780.03650.82389.0087-70.731326.3124
212.0531-2.7263-0.98538.2192-0.71921.2538-0.4251-1.1154-0.47790.33110.35240.32140.3225-0.01670.07670.647-0.13220.16980.7134-0.00440.55991.5708-54.22642.8307
224.6262-2.12860.66178.10916.98647.7540.0607-1.392-0.54291.6927-0.13150.70571.55690.1950.1280.875-0.08570.15970.67210.12810.53076.0768-66.987343.5946
231.2706-1.645-0.1785.77974.88045.83471.1519-0.55560.9415-0.1050.0213-0.2627-0.53331.309-1.19371.52560.25650.35891.20010.21060.714220.4333-73.498541.4437
242.5402-2.7172-2.27872.21512.25041.80350.966-0.34240.5652-1.67440.0347-1.375-0.71921.0496-0.91381.13620.08250.3040.8764-0.12051.151724.6788-68.407427.4143
252.42361.36820.28983.19930.45234.45910.0775-0.0225-0.34260.0545-0.13280.07750.5843-0.14180.05960.44850.0295-0.00780.2096-0.05150.374210.4216-44.176425.7821
264.91284.36940.57628.00974.86019.9453-0.5874-0.3521-0.30790.3560.04380.11770.5492-0.30980.44070.3423-0.02470.08970.2512-0.00630.225811.6628-38.362327.609
271.07312.04440.64769.50593.38232.67190.0396-0.0971-0.47420.79930.0243-0.6470.92250.2813-0.06020.67810.146-0.00690.46140.010.514952.5789-64.939525.4631
283.4597-0.50180.38834.1599-0.65755.3107-0.02470.1946-0.0551-0.32130.069-0.19180.14930.2079-0.05270.29090.0389-0.02080.26750.03820.24844.2348-39.439422.4114
290.69250.2054-0.40724.9942-1.99372.7538-0.02750.13-0.2421-0.3506-0.09720.26590.1418-0.08050.11680.50430.0164-0.02280.3051-0.04490.592925.2097-76.4889-3.3577
306.6683-0.9691-3.16127.06055.2498.62710.07470.64990.769-0.236-0.61171.4966-0.8943-1.25810.49270.5510.03660.01520.33460.050.963915.7987-79.57013.7849
310.3457-0.60940.45926.0838-4.87983.7070.2185-0.0284-0.261-0.09820.14570.67650.11730.0197-0.37620.55130.0337-0.12150.3078-0.01740.426324.4107-62.1437-1.2686
325.1093-1.3739-0.09474.55921.21412.428-0.0941-0.0529-0.2656-0.16730.04980.20580.3820.03160.05650.41710.0416-0.0430.21330.05190.252129.3162-46.0574-1.0536
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 80 )A2 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 115 )A81 - 115
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 164 )A116 - 164
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 206 )A165 - 206
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 276 )A207 - 276
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 95 )B2 - 95
7X-RAY DIFFRACTION7chain 'B' and (resid 96 through 115 )B96 - 115
8X-RAY DIFFRACTION8chain 'B' and (resid 116 through 164 )B116 - 164
9X-RAY DIFFRACTION9chain 'B' and (resid 165 through 206 )B165 - 206
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 245 )B207 - 245
11X-RAY DIFFRACTION11chain 'B' and (resid 246 through 259 )B246 - 259
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 95 )C2 - 95
13X-RAY DIFFRACTION13chain 'C' and (resid 96 through 115 )C96 - 115
14X-RAY DIFFRACTION14chain 'C' and (resid 116 through 154 )C116 - 154
15X-RAY DIFFRACTION15chain 'C' and (resid 155 through 177 )C155 - 177
16X-RAY DIFFRACTION16chain 'C' and (resid 178 through 245 )C178 - 245
17X-RAY DIFFRACTION17chain 'C' and (resid 246 through 259 )C246 - 259
18X-RAY DIFFRACTION18chain 'D' and (resid 5 through 42 )D5 - 42
19X-RAY DIFFRACTION19chain 'D' and (resid 43 through 58 )D43 - 58
20X-RAY DIFFRACTION20chain 'D' and (resid 59 through 80 )D59 - 80
21X-RAY DIFFRACTION21chain 'D' and (resid 81 through 95 )D81 - 95
22X-RAY DIFFRACTION22chain 'D' and (resid 96 through 115 )D96 - 115
23X-RAY DIFFRACTION23chain 'D' and (resid 116 through 154 )D116 - 154
24X-RAY DIFFRACTION24chain 'D' and (resid 155 through 177 )D155 - 177
25X-RAY DIFFRACTION25chain 'D' and (resid 178 through 245 )D178 - 245
26X-RAY DIFFRACTION26chain 'D' and (resid 246 through 259 )D246 - 259
27X-RAY DIFFRACTION27chain 'E' and (resid 2 through 189 )E2 - 189
28X-RAY DIFFRACTION28chain 'E' and (resid 190 through 279 )E190 - 279
29X-RAY DIFFRACTION29chain 'F' and (resid 2 through 115 )F2 - 115
30X-RAY DIFFRACTION30chain 'F' and (resid 116 through 164 )F116 - 164
31X-RAY DIFFRACTION31chain 'F' and (resid 165 through 189 )F165 - 189
32X-RAY DIFFRACTION32chain 'F' and (resid 190 through 260 )F190 - 260

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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://pdbjlvh1.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