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- PDB-8u7j: Crystal Structure of Staphylococcus aureus PLP synthase complex -

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基本情報

登録情報
データベース: PDB / ID: 8u7j
タイトルCrystal Structure of Staphylococcus aureus PLP synthase complex
要素
  • Pyridoxal 5'-phosphate synthase subunit PdxS
  • Pyridoxal 5'-phosphate synthase subunit PdxT
キーワードBIOSYNTHETIC PROTEIN / PLP Synthase complex / Pdx1-Pdx2 / Staphylococcus aureus
機能・相同性
機能・相同性情報


pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / L-glutamine catabolic process / glutaminase / glutaminase activity
類似検索 - 分子機能
Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. ...Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like / Aldolase-type TIM barrel
類似検索 - ドメイン・相同性
GLUTAMINE / PHOSPHATE ION / Pyridoxal 5'-phosphate synthase subunit PdxS / Pyridoxal 5'-phosphate synthase subunit PdxT
類似検索 - 構成要素
生物種Staphylococcus aureus (黄色ブドウ球菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.02 Å
データ登録者Barra, A.L.C. / Brognaro, H. / Betzel, C. / Nascimento, A.S.
資金援助 ブラジル, ドイツ, 9件
組織認可番号
Sao Paulo Research Foundation (FAPESP)2015/26722-8 ブラジル
Sao Paulo Research Foundation (FAPESP)2015/13684-0 ブラジル
Sao Paulo Research Foundation (FAPESP)2020/03983-9 ブラジル
Sao Paulo Research Foundation (FAPESP)2019/26428-3 ブラジル
Sao Paulo Research Foundation (FAPESP)2019/20219-3 ブラジル
Sao Paulo Research Foundation (FAPESP)2019/00899-0 ブラジル
Sao Paulo Research Foundation (FAPESP)2018/21213-6 ブラジル
Brazilian National Council for Scientific and Technological Development (CNPq)302992/2021-9 ブラジル
German Research Foundation (DFG)390715994 ドイツ
引用ジャーナル: J.Biol.Chem. / : 2024
タイトル: Structure and dynamics of the staphylococcal pyridoxal 5-phosphate synthase complex reveal transient interactions at the enzyme interface.
著者: Barra, A.L.C. / Ullah, N. / Brognaro, H. / Gutierrez, R.F. / Wrenger, C. / Betzel, C. / Nascimento, A.S.
履歴
登録2023年9月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年7月24日Provider: repository / タイプ: Initial release
改定 1.12024年7月31日Group: Database references / カテゴリ: citation
Item: _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: Pyridoxal 5'-phosphate synthase subunit PdxS
T: Pyridoxal 5'-phosphate synthase subunit PdxT
G: Pyridoxal 5'-phosphate synthase subunit PdxS
B: Pyridoxal 5'-phosphate synthase subunit PdxS
L: Pyridoxal 5'-phosphate synthase subunit PdxS
K: Pyridoxal 5'-phosphate synthase subunit PdxS
F: Pyridoxal 5'-phosphate synthase subunit PdxS
J: Pyridoxal 5'-phosphate synthase subunit PdxS
C: Pyridoxal 5'-phosphate synthase subunit PdxS
I: Pyridoxal 5'-phosphate synthase subunit PdxS
H: Pyridoxal 5'-phosphate synthase subunit PdxS
D: Pyridoxal 5'-phosphate synthase subunit PdxS
E: Pyridoxal 5'-phosphate synthase subunit PdxS
N: Pyridoxal 5'-phosphate synthase subunit PdxT
S: Pyridoxal 5'-phosphate synthase subunit PdxT
X: Pyridoxal 5'-phosphate synthase subunit PdxT
R: Pyridoxal 5'-phosphate synthase subunit PdxT
W: Pyridoxal 5'-phosphate synthase subunit PdxT
O: Pyridoxal 5'-phosphate synthase subunit PdxT
M: Pyridoxal 5'-phosphate synthase subunit PdxT
V: Pyridoxal 5'-phosphate synthase subunit PdxT
U: Pyridoxal 5'-phosphate synthase subunit PdxT
P: Pyridoxal 5'-phosphate synthase subunit PdxT
Q: Pyridoxal 5'-phosphate synthase subunit PdxT
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)637,91948
ポリマ-635,02524
非ポリマー2,89424
00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)101.235, 132.374, 142.097
Angle α, β, γ (deg.)106.49, 109.51, 105.56
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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要素

#1: タンパク質
Pyridoxal 5'-phosphate synthase subunit PdxS


分子量: 32158.863 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus (黄色ブドウ球菌)
遺伝子: pdxS / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A7WYT1
#2: タンパク質
Pyridoxal 5'-phosphate synthase subunit PdxT


分子量: 20759.867 Da / 分子数: 12 / Mutation: H165N / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus (黄色ブドウ球菌)
遺伝子: pdxT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A7WYT2
#3: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 11 / 由来タイプ: 合成 / : PO4
#4: 化合物
ChemComp-GLN / GLUTAMINE / グルタミン


タイプ: L-peptide linking / 分子量: 146.144 Da / 分子数: 12 / 由来タイプ: 合成 / : C5H10N2O3
#5: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 1 / 由来タイプ: 合成 / : SO4
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: 2.65 Å3/Da / 溶媒含有率: 53.58 %
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 / pH: 7
詳細: 5% PEG4000, 0.2 M triammonium citrate pH 7, 10 mM L-glutamine

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データ収集

回折平均測定温度: 173 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: PETRA III, DESY / ビームライン: P11 / 波長: 1.0332 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2021年8月15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: 1.0332 Å / 相対比: 1
反射解像度: 3.019→116.239 Å / Num. obs: 71124 / % possible obs: 59.3 % / 冗長度: 3.8 % / Biso Wilson estimate: 69.51 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.075 / Net I/σ(I): 4.7
反射 シェル解像度: 3.019→3.389 Å / 冗長度: 3.9 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3556 / CC1/2: 0.76 / Rpim(I) all: 0.329 / % possible all: 10.1

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解析

ソフトウェア
名称バージョン分類
PHENIX(dev_4788: ???)精密化
autoPROCデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.02→54.83 Å / SU ML: 0.33 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 27.03 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2475 3644 5.13 %
Rwork0.1997 --
obs0.2022 71088 59.24 %
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: 3.02→54.83 Å
タンパク質核酸リガンド溶媒全体
原子数39537 0 180 0 39717
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00240209
X-RAY DIFFRACTIONf_angle_d0.45454524
X-RAY DIFFRACTIONf_dihedral_angle_d4.7925796
X-RAY DIFFRACTIONf_chiral_restr0.0426492
X-RAY DIFFRACTIONf_plane_restr0.0037175
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.060.178510.359425X-RAY DIFFRACTION1
3.06-3.10.440260.338180X-RAY DIFFRACTION2
3.1-3.140.798980.3379212X-RAY DIFFRACTION5
3.14-3.190.3736180.3248354X-RAY DIFFRACTION8
3.19-3.240.2019180.3456507X-RAY DIFFRACTION11
3.24-3.290.3737420.3167701X-RAY DIFFRACTION16
3.29-3.350.3833450.2866828X-RAY DIFFRACTION19
3.35-3.410.284600.27051074X-RAY DIFFRACTION24
3.41-3.480.3485680.2611325X-RAY DIFFRACTION30
3.48-3.550.3058980.2451761X-RAY DIFFRACTION40
3.55-3.630.28531180.24782353X-RAY DIFFRACTION53
3.63-3.710.35951270.25222157X-RAY DIFFRACTION50
3.71-3.80.30371900.23853749X-RAY DIFFRACTION85
3.8-3.910.2832140.23184010X-RAY DIFFRACTION91
3.91-4.020.24092380.20524016X-RAY DIFFRACTION92
4.02-4.150.24622250.20273980X-RAY DIFFRACTION91
4.15-4.30.24822090.19073851X-RAY DIFFRACTION89
4.3-4.470.24471870.16623533X-RAY DIFFRACTION80
4.47-4.670.23262260.1623942X-RAY DIFFRACTION91
4.67-4.920.22662200.15584276X-RAY DIFFRACTION97
4.92-5.230.21112080.17494242X-RAY DIFFRACTION97
5.23-5.630.22042080.19484241X-RAY DIFFRACTION96
5.63-6.20.24222290.2214175X-RAY DIFFRACTION95
6.2-7.090.27451960.22344150X-RAY DIFFRACTION94
7.09-8.930.20422210.1843686X-RAY DIFFRACTION85
8.93-54.830.23272640.18784216X-RAY DIFFRACTION97
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.85241.11362.2193.68991.73952.95080.3649-0.603-0.06930.5027-0.23470.5492-0.10820.0271-0.13030.30180.07960.14790.65740.10780.5336-72.6897175.4959290.9089
22.6887-0.16440.47212.3838-2.01524.6723-0.1442-0.12280.67190.14880.12990.2151-0.4489-0.7090.0640.09630.08260.06870.4114-0.01810.6539-92.7608174.5099282.6909
32.945-0.8688-0.65821.9582-1.60252.49670.0828-0.24210.08870.15190.00950.4869-0.4715-0.4757-0.03120.27580.1521-0.00170.2061-0.08240.4532-87.1798181.1943274.7933
40.1689-0.20360.14380.6133-0.22810.271-0.06230.0583-0.10250.02960.0568-0.0154-0.00270.02370.086-0.01910.324-0.07330.31680.02460.3936-72.8233174.8029273.9183
50.2622-0.0949-0.02260.04370.05660.30480.07890.00590.13890.06060.14410.09330.0135-0.03330.1734-0.2220.43970.13890.3758-0.02780.3907-71.1453158.1224279.2787
63.5527-0.6774-1.30771.73181.06681.594-0.07840.10730.2889-0.0530.07680.443-0.2672-0.53590.09790.14410.20380.07650.35070.08070.6954-93.1586162.655282.0976
75.99791.1358-1.26682.93281.00570.98120.1342-0.08620.261-0.2766-0.00450.5963-0.2763-0.8215-0.09530.19390.1723-0.03180.62230.00250.7237-98.5488155.8963286.5079
83.9366-3.9313-1.17424.33311.30593.83820.0388-0.60760.51890.14780.26770.094-0.4041-0.2002-0.21020.1841-0.052-0.04450.4055-0.06390.4416-28.077184.2365280.5895
91.2635-0.6521.11561.9375-0.37041.4741-0.13370.08820.47330.13450.0521-0.302-0.19090.38690.06440.2501-0.1184-0.08630.5179-0.22460.4393-16.7872178.4639282.7026
102.99051.60641.14911.55130.32012.4960.3599-0.8238-0.27580.3119-0.43010.0088-0.2545-0.19950.09570.3194-0.0449-0.14150.9477-0.21780.5189-23.7416171.5512296.0804
113.8831-0.53582.19980.63830.80343.41810.3584-0.96950.22860.9228-0.5371-0.5586-0.108-0.24860.15610.56-0.3352-0.13330.7611-0.09980.5597-21.5179.5466300.7343
126.4956-2.41390.59551.0932-0.97142.89810.4907-0.06450.58690.1862-0.36920.8333-0.2809-0.7816-0.10220.29370.07210.04320.7155-0.06430.6711-29.9033184.4466291.3473
137.0336-0.3518-0.78216.61050.01750.47470.4365-0.86220.42720.5079-0.028-0.2226-0.18450.0791-0.34830.1991-0.04670.01270.8584-0.08190.4816-37.2387167.2815288.3777
143.65420.6785-2.08255.09790.65132.3807-0.2224-0.199-0.31660.361-0.1996-0.76930.05350.63140.22110.0902-0.0533-0.06720.3885-0.07920.2556-21.2109157.2042278.0016
155.68841.12280.63193.38510.03360.1763-0.0084-0.0595-0.28310.18190.0821-0.5624-0.00560.2814-0.22220.00470.0073-0.04290.50890.05190.2743-27.7117148.1645281.563
160.315-0.14180.03420.1083-0.07930.0537-0.0954-0.05430.05550.03480.0481-0.0795-0.00530.0654-0.1361-0.47750.14650.01670.4596-0.1080.3437-41.6239157.2493274.9216
170.6041-0.0530.070.51220.26380.1545-0.0907-0.0928-0.0602-0.0097-0.13010.0841-0.0652-0.0165-0.148-0.04280.0376-0.03350.3544-0.03740.4607-49.2936169.4855271.7126
185.84771.21770.69112.5588-0.83383.822-0.40090.042-0.296-0.16250.0006-0.32360.00740.31660.20610.0765-0.13560.01490.3853-0.08810.3294-22.7288162.802267.6487
198.9292-3.18880.18362.3205-0.7582.37080.21950.2631-0.5933-0.1411-0.1626-0.03480.23590.30380.09610.07960.0551-0.06730.5172-0.03970.6348-17.3087168.9588262.4502
202.72780.05891.44871.53820.82516.0361-0.15590.07631.0855-0.06260.0789-0.0424-0.67180.50010.02870.2743-0.10580.18410.6421-0.0250.9035-55.4621200.9915247.334
217.50692.0285-0.20815.5664-0.29858.20520.24370.55250.2327-0.27890.33630.6022-0.432-0.7499-0.45920.3186-0.0578-0.05040.17730.01830.2477-76.8578199.5577250.8579
222.33840.48291.57494.32764.93456.7621-0.0132-0.11730.3829-0.5621-0.33930.4852-0.8267-0.44020.34490.48630.1130.02540.29290.03690.1655-75.9977196.2451239.6762
232.6357-0.91091.38722.259-2.09313.02320.04310.06310.01340.0080.1785-0.0122-0.3198-0.3254-0.21750.30970.0161-0.00430.2558-0.04290.1698-62.6792187.8654239.2488
240.32770.22270.31951.0314-0.37750.87640.12760.1165-0.064-0.09690.0039-0.0045-0.16110.281-0.0630.13520.0004-0.01790.4313-0.07240.4165-56.7833181.3751254.4907
252.8892-1.3357-1.63182.6568-0.15932.50160.1577-0.25030.2389-0.02570.14320.1401-0.251-0.4409-0.28630.16990.1533-0.07960.3464-0.05920.4506-76.6121192.208263.1693
267.9957-0.41991.3222.79560.13951.8019-0.0126-0.4175-0.63870.10750.06040.31290.1208-0.2863-0.07650.18370.1222-0.11020.59960.10330.6245-62.3088120.496294.2313
272.66050.4578-0.17742.45650.33722.3587-0.1187-0.011-0.62120.3256-0.0054-0.70260.78260.93280.09670.30090.2368-0.07260.44210.08310.656-41.2182120.3465288.9086
283.3458-1.27182.78343.38122.50047.37410.339-0.1057-0.49740.16640.1693-0.51930.57060.9108-0.36970.22080.0954-0.05030.39650.00740.5961-45.7727112.8931281.0678
291.05020.0461-0.21050.4579-0.32230.8669-0.00280.0250.13630.04660.0777-0.0252-0.0269-0.0963-0.076-0.05260.1735-0.03330.3356-0.09780.4536-57.6154115.8696275.9396
300.1390.03630.05290.18350.10280.08060.03860.0318-0.055-0.0187-0.1073-0.05480.02730.0988-0.0013-0.35960.4455-0.15570.31730.0060.4347-62.0127133.3669280.5039
311.63480.96620.96432.3169-0.0511.5476-0.15990.1866-0.3944-0.14010.1248-0.67510.27590.6044-0.130.07960.23810.07070.61650.03120.533-38.8651134.4551288.5927
321.4117-0.6841-0.46762.3112-0.35181.64760.08990.1687-0.6485-0.1875-0.00530.12620.34640.015-0.06030.53330.1704-0.01230.1106-0.10020.5649-60.591991.5069255.3498
332.1603-2.5855-0.20266.246-4.48347.14420.32380.0206-0.195-0.4075-0.2941-0.47010.61970.2089-0.00770.4031-0.0703-0.04550.2593-0.15120.494-51.626494.5076246.342
341.8268-0.5838-1.08180.6778-0.16772.0667-0.4630.0759-0.08580.10270.51790.3150.4562-0.0393-0.04880.38420.0617-0.0370.16640.00340.5064-64.6869102.6788243.2341
350.5832-0.3870.8530.9384-0.29791.31910.0594-0.0085-0.0204-0.09420.17840.24390.21080.0852-0.22440.24480.1085-0.04720.3672-0.03890.593-72.6127110.5716256.8199
362.6313-1.40652.3693.9805-1.07353.30980.14940.3074-0.1308-0.2187-0.0235-0.26670.41350.4901-0.09260.17350.0828-0.04230.2706-0.09580.4164-54.5276100.5734266.0885
372.9093-2.92990.67424.59211.97344.43730.1889-0.05660.2388-0.20110.0841-0.7173-0.01060.3578-0.2770.3940.21130.11220.3597-0.06590.5677-53.7459100.8072275.7653
380.81030.2319-1.67640.7422-1.02144.2215-0.2134-0.4812-0.13380.26310.10170.15770.2775-0.20760.06110.28540.05060.090.95540.00560.9727-96.1373127.693286.3607
393.4527-0.78990.43054.8377-0.65012.6992-0.34290.12910.51680.14370.12970.2783-0.4336-0.54390.22670.18960.0877-0.05960.55820.02390.6337-111.1438136.258273.2038
404.43421.7969-0.64945.09170.53671.77080.3230.01050.72280.01690.21790.5098-0.1078-1.0407-0.49860.23480.0753-0.00520.65990.00830.5859-105.081145.7585276.5883
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1281.1335-0.35-0.67963.0506-0.54743.0896-0.01470.03190.0575-0.74330.0093-0.04270.5058-0.26350.02011.5885-0.2125-0.2230.8305-0.03690.544-87.4433135.0341174.7377
1294.2605-2.9796-2.00224.7656-0.47822.2547-0.1142-0.0181-0.7998-0.32190.2275-0.08660.77450.5743-0.05321.1465-0.0247-0.12181.1732-0.2361.4529-102.2625101.7069217.364
1300.9705-0.6709-0.94311.52430.02771.289-0.13550.3235-0.1435-0.23310.1160.37070.1564-0.6337-0.0081.7578-0.5268-0.55122.02490.00911.4524-114.3628106.0384216.9453
1310.1297-0.22940.50280.5268-0.57772.65910.03260.1769-0.0367-0.26090.12650.3310.3956-0.3816-0.1482.2286-0.9256-0.32832.15890.01391.8654-116.441399.3619231.9919
1321.38471.1564-0.83722.2944-0.85550.52480.4734-0.6834-0.28660.4237-0.15390.4361.0428-0.8642-0.31662.295-1.2862-0.18432.19110.15311.749-118.22391.0597227.4501
1332.4069-2.2142-0.30233.0141-1.0381.8264-0.0545-0.4865-0.1037-0.2179-0.05320.05970.26750.30550.21161.751-0.6325-0.52531.7532-0.27931.673-105.569893.2965223.4979
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 218 )
6X-RAY DIFFRACTION6chain 'A' and (resid 219 through 257 )
7X-RAY DIFFRACTION7chain 'A' and (resid 258 through 275 )
8X-RAY DIFFRACTION8chain 'T' and (resid -1 through 31 )
9X-RAY DIFFRACTION9chain 'T' and (resid 32 through 81 )
10X-RAY DIFFRACTION10chain 'T' and (resid 82 through 137 )
11X-RAY DIFFRACTION11chain 'T' and (resid 138 through 162 )
12X-RAY DIFFRACTION12chain 'T' and (resid 163 through 201 )
13X-RAY DIFFRACTION13chain 'G' and (resid 2 through 18 )
14X-RAY DIFFRACTION14chain 'G' and (resid 19 through 45 )
15X-RAY DIFFRACTION15chain 'G' and (resid 46 through 83 )
16X-RAY DIFFRACTION16chain 'G' and (resid 84 through 177 )
17X-RAY DIFFRACTION17chain 'G' and (resid 178 through 218 )
18X-RAY DIFFRACTION18chain 'G' and (resid 219 through 257 )
19X-RAY DIFFRACTION19chain 'G' and (resid 258 through 275 )
20X-RAY DIFFRACTION20chain 'B' and (resid 2 through 18 )
21X-RAY DIFFRACTION21chain 'B' and (resid 19 through 45 )
22X-RAY DIFFRACTION22chain 'B' and (resid 46 through 83 )
23X-RAY DIFFRACTION23chain 'B' and (resid 84 through 142 )
24X-RAY DIFFRACTION24chain 'B' and (resid 143 through 218 )
25X-RAY DIFFRACTION25chain 'B' and (resid 219 through 275 )
26X-RAY DIFFRACTION26chain 'L' and (resid 2 through 18 )
27X-RAY DIFFRACTION27chain 'L' and (resid 19 through 45 )
28X-RAY DIFFRACTION28chain 'L' and (resid 46 through 83 )
29X-RAY DIFFRACTION29chain 'L' and (resid 84 through 118 )
30X-RAY DIFFRACTION30chain 'L' and (resid 119 through 218 )
31X-RAY DIFFRACTION31chain 'L' and (resid 219 through 275 )
32X-RAY DIFFRACTION32chain 'K' and (resid 2 through 45 )
33X-RAY DIFFRACTION33chain 'K' and (resid 46 through 83 )
34X-RAY DIFFRACTION34chain 'K' and (resid 84 through 142 )
35X-RAY DIFFRACTION35chain 'K' and (resid 143 through 218 )
36X-RAY DIFFRACTION36chain 'K' and (resid 219 through 257 )
37X-RAY DIFFRACTION37chain 'K' and (resid 258 through 275 )
38X-RAY DIFFRACTION38chain 'F' and (resid 2 through 18 )
39X-RAY DIFFRACTION39chain 'F' and (resid 19 through 45 )
40X-RAY DIFFRACTION40chain 'F' and (resid 46 through 83 )
41X-RAY DIFFRACTION41chain 'F' and (resid 84 through 142 )
42X-RAY DIFFRACTION42chain 'F' and (resid 143 through 218 )
43X-RAY DIFFRACTION43chain 'F' and (resid 219 through 257 )
44X-RAY DIFFRACTION44chain 'F' and (resid 258 through 275 )
45X-RAY DIFFRACTION45chain 'J' and (resid 2 through 45 )
46X-RAY DIFFRACTION46chain 'J' and (resid 46 through 83 )
47X-RAY DIFFRACTION47chain 'J' and (resid 84 through 142 )
48X-RAY DIFFRACTION48chain 'J' and (resid 143 through 218 )
49X-RAY DIFFRACTION49chain 'J' and (resid 219 through 257 )
50X-RAY DIFFRACTION50chain 'J' and (resid 258 through 275 )
51X-RAY DIFFRACTION51chain 'C' and (resid 2 through 18 )
52X-RAY DIFFRACTION52chain 'C' and (resid 19 through 45 )
53X-RAY DIFFRACTION53chain 'C' and (resid 46 through 83 )
54X-RAY DIFFRACTION54chain 'C' and (resid 84 through 142 )
55X-RAY DIFFRACTION55chain 'C' and (resid 143 through 193 )
56X-RAY DIFFRACTION56chain 'C' and (resid 194 through 218 )
57X-RAY DIFFRACTION57chain 'C' and (resid 219 through 257 )
58X-RAY DIFFRACTION58chain 'C' and (resid 258 through 275 )
59X-RAY DIFFRACTION59chain 'I' and (resid 2 through 18 )
60X-RAY DIFFRACTION60chain 'I' and (resid 19 through 45 )
61X-RAY DIFFRACTION61chain 'I' and (resid 46 through 83 )
62X-RAY DIFFRACTION62chain 'I' and (resid 84 through 142 )
63X-RAY DIFFRACTION63chain 'I' and (resid 143 through 218 )
64X-RAY DIFFRACTION64chain 'I' and (resid 219 through 275 )
65X-RAY DIFFRACTION65chain 'H' and (resid 2 through 18 )
66X-RAY DIFFRACTION66chain 'H' and (resid 19 through 45 )
67X-RAY DIFFRACTION67chain 'H' and (resid 46 through 83 )
68X-RAY DIFFRACTION68chain 'H' and (resid 84 through 142 )
69X-RAY DIFFRACTION69chain 'H' and (resid 143 through 228 )
70X-RAY DIFFRACTION70chain 'H' and (resid 229 through 275 )
71X-RAY DIFFRACTION71chain 'D' and (resid 2 through 18 )
72X-RAY DIFFRACTION72chain 'D' and (resid 19 through 45 )
73X-RAY DIFFRACTION73chain 'D' and (resid 46 through 83 )
74X-RAY DIFFRACTION74chain 'D' and (resid 84 through 142 )
75X-RAY DIFFRACTION75chain 'D' and (resid 143 through 218 )
76X-RAY DIFFRACTION76chain 'D' and (resid 219 through 275 )
77X-RAY DIFFRACTION77chain 'E' and (resid 2 through 18 )
78X-RAY DIFFRACTION78chain 'E' and (resid 19 through 45 )
79X-RAY DIFFRACTION79chain 'E' and (resid 46 through 84 )
80X-RAY DIFFRACTION80chain 'E' and (resid 85 through 177 )
81X-RAY DIFFRACTION81chain 'E' and (resid 178 through 218 )
82X-RAY DIFFRACTION82chain 'E' and (resid 219 through 275 )
83X-RAY DIFFRACTION83chain 'N' and (resid -1 through 31 )
84X-RAY DIFFRACTION84chain 'N' and (resid 32 through 81 )
85X-RAY DIFFRACTION85chain 'N' and (resid 82 through 137 )
86X-RAY DIFFRACTION86chain 'N' and (resid 138 through 201 )
87X-RAY DIFFRACTION87chain 'S' and (resid -1 through 31 )
88X-RAY DIFFRACTION88chain 'S' and (resid 32 through 65 )
89X-RAY DIFFRACTION89chain 'S' and (resid 66 through 81 )
90X-RAY DIFFRACTION90chain 'S' and (resid 82 through 137 )
91X-RAY DIFFRACTION91chain 'S' and (resid 138 through 162 )
92X-RAY DIFFRACTION92chain 'S' and (resid 163 through 201 )
93X-RAY DIFFRACTION93chain 'X' and (resid -1 through 31 )
94X-RAY DIFFRACTION94chain 'X' and (resid 32 through 81 )
95X-RAY DIFFRACTION95chain 'X' and (resid 82 through 137 )
96X-RAY DIFFRACTION96chain 'X' and (resid 138 through 201 )
97X-RAY DIFFRACTION97chain 'R' and (resid -1 through 31 )
98X-RAY DIFFRACTION98chain 'R' and (resid 32 through 81 )
99X-RAY DIFFRACTION99chain 'R' and (resid 82 through 137 )
100X-RAY DIFFRACTION100chain 'R' and (resid 138 through 162 )
101X-RAY DIFFRACTION101chain 'R' and (resid 163 through 201 )
102X-RAY DIFFRACTION102chain 'W' and (resid -1 through 31 )
103X-RAY DIFFRACTION103chain 'W' and (resid 32 through 81 )
104X-RAY DIFFRACTION104chain 'W' and (resid 82 through 137 )
105X-RAY DIFFRACTION105chain 'W' and (resid 138 through 162 )
106X-RAY DIFFRACTION106chain 'W' and (resid 163 through 201 )
107X-RAY DIFFRACTION107chain 'O' and (resid -1 through 31 )
108X-RAY DIFFRACTION108chain 'O' and (resid 32 through 81 )
109X-RAY DIFFRACTION109chain 'O' and (resid 82 through 137 )
110X-RAY DIFFRACTION110chain 'O' and (resid 138 through 162 )
111X-RAY DIFFRACTION111chain 'O' and (resid 163 through 201 )
112X-RAY DIFFRACTION112chain 'M' and (resid -1 through 31 )
113X-RAY DIFFRACTION113chain 'M' and (resid 32 through 81 )
114X-RAY DIFFRACTION114chain 'M' and (resid 82 through 137 )
115X-RAY DIFFRACTION115chain 'M' and (resid 138 through 201 )
116X-RAY DIFFRACTION116chain 'V' and (resid -1 through 31 )
117X-RAY DIFFRACTION117chain 'V' and (resid 32 through 81 )
118X-RAY DIFFRACTION118chain 'V' and (resid 82 through 137 )
119X-RAY DIFFRACTION119chain 'V' and (resid 138 through 201 )
120X-RAY DIFFRACTION120chain 'U' and (resid -1 through 31 )
121X-RAY DIFFRACTION121chain 'U' and (resid 32 through 81 )
122X-RAY DIFFRACTION122chain 'U' and (resid 82 through 137 )
123X-RAY DIFFRACTION123chain 'U' and (resid 138 through 162 )
124X-RAY DIFFRACTION124chain 'U' and (resid 163 through 201 )
125X-RAY DIFFRACTION125chain 'P' and (resid -1 through 31 )
126X-RAY DIFFRACTION126chain 'P' and (resid 32 through 81 )
127X-RAY DIFFRACTION127chain 'P' and (resid 82 through 137 )
128X-RAY DIFFRACTION128chain 'P' and (resid 138 through 201 )
129X-RAY DIFFRACTION129chain 'Q' and (resid -1 through 31 )
130X-RAY DIFFRACTION130chain 'Q' and (resid 32 through 81 )
131X-RAY DIFFRACTION131chain 'Q' and (resid 82 through 137 )
132X-RAY DIFFRACTION132chain 'Q' and (resid 138 through 162 )
133X-RAY DIFFRACTION133chain 'Q' and (resid 163 through 201 )

+
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

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月:コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか? / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例:em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る