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- PDB-7s5e: Crystal structure of a guanylate kinase from Stenotrophomonas mal... -

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基本情報

登録情報
データベース: PDB / ID: 7s5e
タイトルCrystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a with heterogeneous ligand states of GMP/ADP, GMP/-, GDP/-, and GMP/ATPgS
要素Guanylate kinase
キーワードTRANSFERASE (転移酵素) / NIAID / structural genomics (構造ゲノミクス) / global emerging Gram-negative MDRO / guanylate kinase / Seattle Structural Genomics Center for Infectious Disease / SSGCID
機能・相同性
機能・相同性情報


guanylate kinase / guanylate kinase activity / リン酸化 / ATP binding / 細胞質
類似検索 - 分子機能
Guanylate kinase / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
GUANOSINE-5'-MONOPHOSPHATE / ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / Guanylate kinase
類似検索 - 構成要素
生物種Stenotrophomonas maltophilia (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: 2.4 Å
データ登録者Seattle Structural Genomics Center for Infectious Disease (SSGCID)
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 米国
引用ジャーナル: To Be Published
タイトル: Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279c with heterogeneous ligand states of GMP/ADP, GMP/-, GDP/-, and GMP/ATPgS.
著者: Edwards, T.E. / Horanyi, P.S. / Abendroth, J. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
履歴
登録2021年9月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年9月22日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Guanylate kinase
B: Guanylate kinase
C: Guanylate kinase
D: Guanylate kinase
E: Guanylate kinase
F: Guanylate kinase
G: Guanylate kinase
H: Guanylate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)206,66620
ポリマ－201,7008
非ポリマー4,96712
水6,792377
1
A: Guanylate kinase
C: Guanylate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,6595
ポリマ－50,4252
非ポリマー1,2343
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-36 kcal/mol
Surface area18160 Å2
手法PISA
2
B: Guanylate kinase
D: Guanylate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,6755
ポリマ－50,4252
非ポリマー1,2503
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-31 kcal/mol
Surface area18790 Å2
手法PISA
3
E: Guanylate kinase
G: Guanylate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,6595
ポリマ－50,4252
非ポリマー1,2343
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-36 kcal/mol
Surface area18200 Å2
手法PISA
4
F: Guanylate kinase
H: Guanylate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,6755
ポリマ－50,4252
非ポリマー1,2503
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-29 kcal/mol
Surface area18840 Å2
手法PISA
単位格子
Length a, b, c (Å)97.160, 100.530, 92.250
Angle α, β, γ (deg.)90.000, 95.210, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and ((resid 12 through 13 and (name N...
21(chain B and (resid 12 through 67 or (resid 68...
31(chain C and ((resid 12 through 13 and (name N...
41(chain D and ((resid 12 through 13 and (name N...
51(chain E and ((resid 12 through 13 and (name N...
61(chain F and (resid 12 through 67 or (resid 68...
71(chain G and (resid 12 through 26 or (resid 27...
81(chain H and ((resid 12 through 13 and (name N...

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
11ALAALAARGARG(chain A and ((resid 12 through 13 and (name N...AA12 - 1320 - 21
12ALAALAADPADP(chain A and ((resid 12 through 13 and (name N...AA - J12 - 30220
13ALAALAADPADP(chain A and ((resid 12 through 13 and (name N...AA - J12 - 30220
14ALAALAADPADP(chain A and ((resid 12 through 13 and (name N...AA - J12 - 30220
15ALAALAADPADP(chain A and ((resid 12 through 13 and (name N...AA - J12 - 30220
21ALAALAALAALA(chain B and (resid 12 through 67 or (resid 68...BB12 - 6720 - 75
22GLUGLULYSLYS(chain B and (resid 12 through 67 or (resid 68...BB68 - 6976 - 77
23VALVAL5GP5GP(chain B and (resid 12 through 67 or (resid 68...BB - K11 - 30119
24VALVAL5GP5GP(chain B and (resid 12 through 67 or (resid 68...BB - K11 - 30119
25VALVAL5GP5GP(chain B and (resid 12 through 67 or (resid 68...BB - K11 - 30119
26VALVAL5GP5GP(chain B and (resid 12 through 67 or (resid 68...BB - K11 - 30119
31ALAALAARGARG(chain C and ((resid 12 through 13 and (name N...CC12 - 1320 - 21
32ALAALAGDPGDP(chain C and ((resid 12 through 13 and (name N...CC - L12 - 30120
33ALAALAGDPGDP(chain C and ((resid 12 through 13 and (name N...CC - L12 - 30120
34ALAALAGDPGDP(chain C and ((resid 12 through 13 and (name N...CC - L12 - 30120
35ALAALAGDPGDP(chain C and ((resid 12 through 13 and (name N...CC - L12 - 30120
41ALAALAARGARG(chain D and ((resid 12 through 13 and (name N...DD12 - 1320 - 21
42ALAALAAGSAGS(chain D and ((resid 12 through 13 and (name N...DD - N10 - 30218
43ALAALAAGSAGS(chain D and ((resid 12 through 13 and (name N...DD - N10 - 30218
51ALAALAARGARG(chain E and ((resid 12 through 13 and (name N...EE12 - 1320 - 21
52ALAALAADPADP(chain E and ((resid 12 through 13 and (name N...EE - P12 - 30220
53ALAALAADPADP(chain E and ((resid 12 through 13 and (name N...EE - P12 - 30220
54ALAALAADPADP(chain E and ((resid 12 through 13 and (name N...EE - P12 - 30220
55ALAALAADPADP(chain E and ((resid 12 through 13 and (name N...EE - P12 - 30220
61ALAALAALAALA(chain F and (resid 12 through 67 or (resid 68...FF12 - 6720 - 75
62GLUGLULYSLYS(chain F and (resid 12 through 67 or (resid 68...FF68 - 6976 - 77
63VALVAL5GP5GP(chain F and (resid 12 through 67 or (resid 68...FF - Q11 - 30119
64VALVAL5GP5GP(chain F and (resid 12 through 67 or (resid 68...FF - Q11 - 30119
65VALVAL5GP5GP(chain F and (resid 12 through 67 or (resid 68...FF - Q11 - 30119
66VALVAL5GP5GP(chain F and (resid 12 through 67 or (resid 68...FF - Q11 - 30119
71ALAALAGLYGLY(chain G and (resid 12 through 26 or (resid 27...GG12 - 2620 - 34
72LYSLYSLYSLYS(chain G and (resid 12 through 26 or (resid 27...GG2735
73ALAALAGDPGDP(chain G and (resid 12 through 26 or (resid 27...GG - R12 - 30120
74ALAALAGDPGDP(chain G and (resid 12 through 26 or (resid 27...GG - R12 - 30120
75ALAALAGDPGDP(chain G and (resid 12 through 26 or (resid 27...GG - R12 - 30120
76ALAALAGDPGDP(chain G and (resid 12 through 26 or (resid 27...GG - R12 - 30120
81ALAALAARGARG(chain H and ((resid 12 through 13 and (name N...HH12 - 1320 - 21
82ALAALAAGSAGS(chain H and ((resid 12 through 13 and (name N...HH - T10 - 30218
83ALAALAAGSAGS(chain H and ((resid 12 through 13 and (name N...HH - T10 - 30218

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要素

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タンパク質 , 1種, 8分子 ABCDEFGH

#1: タンパク質
Guanylate kinase / / GMP kinase


分子量: 25212.443 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Stenotrophomonas maltophilia (strain K279a) (バクテリア)
株: K279a / 遺伝子: gmk, Smlt3842 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: B2FT06, guanylate kinase

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非ポリマー , 5種, 389分子

#2: 化合物
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / GMP / グアニル酸


分子量: 363.221 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H14N5O8P / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物 ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP / アデノシン二リン酸


分子量: 427.201 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: ADP, エネルギー貯蔵分子*YM
#4: 化合物 ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP / グアノシン二リン酸


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: GDP, エネルギー貯蔵分子*YM
#5: 化合物 ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE / ATP-γ-S


分子量: 523.247 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H16N5O12P3S / タイプ: SUBJECT OF INVESTIGATION
コメント: ATP-gamma-S, エネルギー貯蔵分子類似体*YM
#6: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 377 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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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: 2.23 Å3/Da / 溶媒含有率: 44.8 %
結晶化温度: 287 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.2
詳細: StmaA.01463.a.B1.PW38755 at 33 mg/mL with 4 mM 5GP (GMP) and 4 mM ATPgS (AGS) against MCSG1 B1 focus screen condition B4: 0.1 M MES pH 6.2, 18% PEG 4000, 0.6 M NaCl, supplemented with 20% EG ...詳細: StmaA.01463.a.B1.PW38755 at 33 mg/mL with 4 mM 5GP (GMP) and 4 mM ATPgS (AGS) against MCSG1 B1 focus screen condition B4: 0.1 M MES pH 6.2, 18% PEG 4000, 0.6 M NaCl, supplemented with 20% EG as cryo with 4 mM 5GP and 4 mM AGS, unique puck ID kjd4-1, 318570b4

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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: APS / ビームライン: 21-ID-F / 波長: 0.97872 Å
検出器タイプ: RAYONIX MX300-HS / 検出器: CCD / 日付: 2020年11月5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: 0.97872 Å / 相対比: 1
反射解像度: 2.4→45.93 Å / Num. obs: 66984 / % possible obs: 96.8 % / 冗長度: 3.852 % / Biso Wilson estimate: 41.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.083 / Χ2: 0.83 / Net I/σ(I): 9.62 / Num. measured all: 258053 / Scaling rejects: 4037
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.463.8940.6382.2319343511149670.9130.7497.2
2.46-2.533.890.5492.5218763494348230.9470.63797.6
2.53-2.63.8920.4792.8518421484847330.9510.55697.6
2.6-2.683.8880.3943.3717836469245880.9640.45697.8
2.68-2.773.8840.3243.9717317455744590.9770.37597.8
2.77-2.873.8780.2594.8716694440043050.9830.397.8
2.87-2.983.8730.1876.3316117428041610.990.21797.2
2.98-3.13.870.1447.6915304405639550.9940.16897.5
3.1-3.243.8590.1159.1314721393838150.9960.13396.9
3.24-3.393.850.08311.1613958374536250.9980.09796.8
3.39-3.583.8290.06912.9613237357734570.9980.0896.6
3.58-3.793.8210.05414.8512395337632440.9990.06396.1
3.79-4.063.8170.04417.1911245317729460.9990.05192.7
4.06-4.383.810.03619.4310572299827750.9990.04292.6
4.38-4.83.8130.03320.49582270525130.9990.03892.9
4.8-5.373.8240.03719.429178248524000.9990.04396.6
5.37-6.23.8130.03618.758209219221530.9990.04298.2
6.2-7.593.7930.03219.86964186018360.9990.03898.7
7.59-10.733.7610.02522.395404145614370.9990.02998.7
10.73-45.933.5270.02421.9727938197920.9990.02896.7

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XSCALEデータスケーリング
MOLREP位相決定
PHENIXdev-4274精密化
PDB_EXTRACT3.27データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 6wct

6wct


解像度: 2.4→45.93 Å / SU ML: 0.31 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 44.48 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2647 2036 3.07 %
Rwork0.2259 64334 -
obs0.227 66370 95.92 %
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
原子変位パラメータBiso max: 125.57 Å2 / Biso mean: 53.3726 Å2 / Biso min: 31.11 Å2
精密化ステップサイクル: final / 解像度: 2.4→45.93 Å
タンパク質核酸リガンド溶媒全体
原子数12088 0 316 377 12781
Biso mean--48.85 47.24 -
残基数----1612
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A6701X-RAY DIFFRACTION5.342TORSIONAL
12B6701X-RAY DIFFRACTION5.342TORSIONAL
13C6701X-RAY DIFFRACTION5.342TORSIONAL
14D6701X-RAY DIFFRACTION5.342TORSIONAL
15E6701X-RAY DIFFRACTION5.342TORSIONAL
16F6701X-RAY DIFFRACTION5.342TORSIONAL
17G6701X-RAY DIFFRACTION5.342TORSIONAL
18H6701X-RAY DIFFRACTION5.342TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.37361690.33284298446797
2.46-2.520.31361330.32434311444497
2.52-2.590.37551580.33034305446397
2.59-2.660.33281290.31744339446897
2.66-2.750.38131200.31384340446097
2.75-2.850.2981330.29324394452798
2.85-2.960.32151330.26984330446397
2.96-3.090.28021570.24794297445497
3.09-3.260.29491190.25824333445296
3.26-3.460.32081340.23484326446097
3.46-3.730.28011410.21084305444697
3.73-4.10.22481330.19084161429493
4.1-4.70.19631310.16454144427592
4.7-5.910.19921340.18244362449696
5.92-45.930.17971120.17194089420189
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)
17.1416-0.38723.80843.22411.84474.2392-0.2312-0.49440.51480.1233-0.0916-0.0153-0.2772-0.19830.44170.43120.01280.12020.35250.03660.470110.38384.82080.2456
21.70110.6065-1.0153.3030.99053.3750.2198-0.3572-0.08540.3882-0.05750.1041-0.4110.0361-0.04090.56670.00460.12680.2420.0220.5242-2.13937.258310.1759
32.2425-0.253-0.90510.45950.92442.3924-0.09280.1918-0.1093-0.1255-0.18060.20360.1864-0.29450.27120.55090.00860.12220.2735-0.0530.55530.79342.1482-0.4612
46.5268-0.0786-3.88871.5173-2.11055.40170.2742-0.92980.88881.19270.4522-0.2796-0.91061.09540.40170.54650.0119-0.05840.64620.07540.422316.0079-4.849118.13
51.8033-0.695-1.10391.81960.02246.12010.13370.1328-0.0587-0.0159-0.04160.198-0.6673-0.1748-0.13110.291-0.0515-0.03730.30960.00420.427911.6339-0.6662-5.0125
62.284-0.2636-0.09832.94580.47767.59310.25020.7646-0.0492-0.0212-0.39360.48370.3497-1.37760.21390.5511-0.08430.05430.9466-0.03970.287242.8542-20.0304-0.0641
78.26580.5233-4.25737.0403-2.10159.2113-0.14480.6926-0.4994-1.06410.18521.08560.5909-1.6513-0.3360.5488-0.064-0.05060.91310.11360.448343.7692-14.79-10.5865
87.35580.7875-1.57443.8002-2.34326.164-0.14650.789-0.05860.08020.4640.2306-0.2746-0.9616-0.26460.56710.15380.04580.73060.03340.290448.9032-8.2231-12.1671
93.6361-0.3628-1.06663.34-1.75864.99420.14470.8831-0.4306-0.1377-0.25170.3024-0.3711-1.03860.01110.4787-0.17070.04460.5433-0.03760.219251.6074-17.9248-0.3488
105.1489-0.7901-2.43221.8510.56771.809-0.08070.7891-0.14690.0314-0.0737-0.01830.0594-0.70520.19690.4824-0.0606-0.0470.56050.06140.211145.995-18.84697.3148
113.177-1.08030.13373.65382.05431.74110.20170.22610.1875-0.2917-0.3364-0.2473-0.04670.5042-0.08390.5034-0.09410.18460.686-0.01520.441125.388-2.0075-22.3643
124.79991.4322-0.90215.6991.58585.68950.4122-0.64740.17830.12940.32090.0134-0.72170.5597-0.60150.25270.034-0.00070.31440.10490.449229.8321-12.5421-35.0305
136.4741-0.22251.66453.9423.39185.0243-0.0505-0.6214-0.21430.68590.110.50090.95530.2863-0.18040.67380.11560.25910.35890.04480.463726.3692-16.4062-28.25
142.0893-0.8263-2.26552.52463.48976.6028-0.0577-0.4665-0.030.185-0.33080.44960.027-0.06020.20360.4198-0.05940.10110.5832-0.06370.594718.687-7.8771-25.5992
152.6539-0.77250.23341.03270.83293.4741-0.04850.58140.0123-0.46350.0397-0.0911-0.44130.30170.1750.64430.00870.13230.33380.01970.476517.9366-0.8278-19.4698
161.1876-0.2912-0.37792.4409-0.60311.7303-0.1980.22470.0087-0.1647-0.0230.24270.2092-0.24230.04480.5045-0.12210.09470.54910.02090.546637.9165-24.975925.5558
173.0940.2648-0.66613.96270.9125.4257-0.60360.1151-0.43360.0756-0.36970.16721.052-0.4024-0.29860.18630.1246-0.1120.10460.11370.18141.4659-25.634643.1791
183.48670.94341.32571.7251-0.42933.7328-0.72780.30290.0148-0.5320.4565-0.14590.77620.71910.35450.3655-0.06220.18790.48060.11960.384148.5034-25.842837.6586
191.2519-0.6907-0.46141.45560.29783.8353-0.14-0.04450.10810.08190.0288-0.0992-0.1262-0.16610.2270.4826-0.08440.02760.40190.00410.3534.9651-17.686630.2232
200.14710.6741-0.51293.0577-1.81894.2227-0.4651-0.2307-0.6959-0.6326-0.3271-0.93170.3380.44080.75750.7086-0.03310.08650.38790.04250.449828.9061-11.172135.1062
215.6473-0.1009-2.47761.0847-0.32141.435-0.05690.7624-0.1097-0.1030.06530.005-0.093-0.2827-0.05810.5299-0.03370.04730.36720.00580.237245.8991-23.811414.3103
223.4325-0.2788-0.80984.7110.30051.6239-0.0942-0.160.3212-0.32920.4302-0.3193-0.34220.0484-0.26620.5292-0.11470.11990.3262-0.14570.238354.77044.824846.1796
234.18030.3769-1.73425.28370.78472.31970.3512-0.32150.45570.5406-0.1371-0.1961-0.49970.4038-0.29350.6027-0.00310.06910.4267-0.06330.307847.50979.861656.8102
244.9546-0.3397-2.44141.4461.08431.77510.01230.16970.52970.0514-0.11170.3286-0.1145-0.2051-0.1160.44460.01850.09320.3410.01170.551436.9665.608651.9542
252.5481-0.4728-1.42623.12120.65521.01790.18510.25230.2930.23580.09750.3185-0.6360.1847-0.18470.36250.0076-0.0560.38690.04010.244347.7741-0.73144.4983
261.3742-0.52950.80590.22010.237.7761-0.0286-0.53340.0391-0.1917-0.0636-0.1629-1.29680.43550.08910.69850.01880.04530.45390.01920.312355.2434-7.669260.4823
272.1841-0.0738-1.4511.29540.8295.4907-0.06350.33450.1914-0.4355-0.0779-0.0224-0.3844-0.61980.0890.66110.12890.09250.3216-0.05960.377758.1223.601333.1831
286.7049-1.13840.89733.0187-2.47562.00830.12051.4301-0.74740.0913-0.0890.00420.3239-1.53570.15240.4291-0.13650.07610.9123-0.08390.381187.2415-20.044145.8641
298.86812.2608-2.74618.2649-2.9297.44370.00161.0693-0.1676-0.36210.43650.3902-0.095-1.3203-0.46020.58230.08310.00570.75240.04420.344792.8113-10.77832.6401
303.213-0.309-0.5772.8183-2.25884.78710.13290.41460.12960.0937-0.00830.013-0.6154-0.687-0.06960.44050.07180.05870.6460.03190.326694.2084-14.646844.0297
316.3688-2.6811-4.10572.5792.56265.1520.13210.5978-0.0381-0.2177-0.1091-0.0783-0.1316-0.4715-0.0340.3176-0.03370.0080.44570.06350.358590.3884-18.849453.2522
325.1594-2.10731.48092.9261.91174.16020.10010.15820.48190.20310.0585-0.2533-0.99070.2609-0.0240.6177-0.09710.18180.4841-0.05410.473869.9321-1.415623.3403
336.0653-0.5895-1.57494.7423-0.89860.64350.3706-1.1638-0.38130.9482-0.0826-0.2450.28280.02670.02890.4908-0.13210.00120.68910.03140.361574.5593-9.200122.3703
345.97341.04110.08091.6304-0.56841.9031-0.00070.32920.11410.3319-0.26120.24410.5103-0.21050.31530.5282-0.00470.15890.3289-0.0750.383274.1271-13.42167.8764
358.196-1.10310.436.10190.28980.8563-0.2342-0.8396-0.4470.82030.67130.5170.77130.9037-0.13430.53140.052-0.0350.4294-0.03620.353770.5886-16.441517.4121
363.14380.7598-1.11494.41082.94815.16470.4491-0.86430.5363-0.0524-0.66570.4577-0.1236-0.31420.4610.4932-0.04810.18470.5701-0.11590.372364.0527-10.271819.375
372.3859-0.3728-0.21473.36012.25723.7630.03860.6675-0.0622-0.0927-0.26230.13250.2441-0.46130.21360.7262-0.0117-0.00770.49810.03870.120861.1677-3.177322.241
380.9621-0.95961.57371.7808-0.64633.6205-0.81911.1154-0.1968-0.1753-0.6646-0.9168-0.9218-0.13411.21841.7132-0.31690.14221.11570.16660.670865.929313.72349.5892
393.3078-1.38261.34352.56011.43564.5186-0.32831.61960.2084-0.6112-0.3158-0.5366-1.1616-0.32920.53820.92650.15770.02930.86390.11480.469160.49743.55647.5351
405.1656-1.48360.10172.680.11017.83860.40950.38530.82510.1245-0.2582-0.2496-0.80280.1293-0.15610.4747-0.04170.0340.4501-0.01710.327964.91083.172428.3927
412.9767-0.1073-0.42713.3627-1.13694.71260.101-0.2894-0.0615-0.39470.2646-0.25230.59470.5946-0.24820.3371-0.0332-0.06270.5177-0.05960.296759.159-15.250246.3235
421.5538-0.99710.25381.7139-0.41782.6389-0.107-0.1220.0047-0.26530.0711-0.18070.1743-0.09540.19390.3895-0.1029-0.02590.32960.07220.29482.3148-25.03971.5272
431.57410.22450.59292.1887-0.13681.3821-0.00450.0690.00210.32740.28080.1138-0.21040.1004-0.14910.6378-0.01960.18910.27970.0230.567985.8776-25.655389.1176
441.77090.40141.07510.8864-0.98953.0172-0.28350.26180.57450.2361-0.0399-0.02510.47840.54720.27250.5359-0.02760.1240.3399-0.06940.508492.8643-25.827983.49
450.9876-0.06770.58780.32490.40443.9127-0.25620.30020.37780.30990.0496-0.0718-0.39110.09350.09670.54180.00590.1350.34890.0610.489286.9133-17.558175.3621
460.17360.46490.08251.4562-0.97454.53570.1871-0.060.49550.4892-0.35810.22550.0176-0.48370.08920.61740.05410.0860.5351-0.0230.416868.6384-14.201779.6489
477.6121-2.1494-3.53022.44250.7343.106-0.06810.2473-0.4374-0.1553-0.1333-0.06190.5287-0.5370.12630.3643-0.07960.05040.4283-0.01720.366490.284-23.816760.2407
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 37 )A12 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 87 )A38 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 135 )A88 - 135
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 150 )A136 - 150
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 214 )A151 - 214
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 37 )B11 - 37
7X-RAY DIFFRACTION7chain 'B' and (resid 38 through 53 )B38 - 53
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 102 )B54 - 102
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 150 )B103 - 150
10X-RAY DIFFRACTION10chain 'B' and (resid 151 through 214 )B151 - 214
11X-RAY DIFFRACTION11chain 'C' and (resid 12 through 37 )C12 - 37
12X-RAY DIFFRACTION12chain 'C' and (resid 38 through 87 )C38 - 87
13X-RAY DIFFRACTION13chain 'C' and (resid 88 through 102 )C88 - 102
14X-RAY DIFFRACTION14chain 'C' and (resid 103 through 133 )C103 - 133
15X-RAY DIFFRACTION15chain 'C' and (resid 134 through 216 )C134 - 216
16X-RAY DIFFRACTION16chain 'D' and (resid 10 through 37 )D10 - 37
17X-RAY DIFFRACTION17chain 'D' and (resid 38 through 87 )D38 - 87
18X-RAY DIFFRACTION18chain 'D' and (resid 88 through 102 )D88 - 102
19X-RAY DIFFRACTION19chain 'D' and (resid 103 through 150 )D103 - 150
20X-RAY DIFFRACTION20chain 'D' and (resid 151 through 170 )D151 - 170
21X-RAY DIFFRACTION21chain 'D' and (resid 171 through 216 )D171 - 216
22X-RAY DIFFRACTION22chain 'E' and (resid 12 through 37 )E12 - 37
23X-RAY DIFFRACTION23chain 'E' and (resid 38 through 66 )E38 - 66
24X-RAY DIFFRACTION24chain 'E' and (resid 67 through 102 )E67 - 102
25X-RAY DIFFRACTION25chain 'E' and (resid 103 through 135 )E103 - 135
26X-RAY DIFFRACTION26chain 'E' and (resid 136 through 170 )E136 - 170
27X-RAY DIFFRACTION27chain 'E' and (resid 171 through 214 )E171 - 214
28X-RAY DIFFRACTION28chain 'F' and (resid 11 through 37 )F11 - 37
29X-RAY DIFFRACTION29chain 'F' and (resid 38 through 87 )F38 - 87
30X-RAY DIFFRACTION30chain 'F' and (resid 88 through 150 )F88 - 150
31X-RAY DIFFRACTION31chain 'F' and (resid 151 through 214 )F151 - 214
32X-RAY DIFFRACTION32chain 'G' and (resid 12 through 37 )G12 - 37
33X-RAY DIFFRACTION33chain 'G' and (resid 38 through 48 )G38 - 48
34X-RAY DIFFRACTION34chain 'G' and (resid 49 through 87 )G49 - 87
35X-RAY DIFFRACTION35chain 'G' and (resid 88 through 102 )G88 - 102
36X-RAY DIFFRACTION36chain 'G' and (resid 103 through 122 )G103 - 122
37X-RAY DIFFRACTION37chain 'G' and (resid 123 through 133 )G123 - 133
38X-RAY DIFFRACTION38chain 'G' and (resid 134 through 150 )G134 - 150
39X-RAY DIFFRACTION39chain 'G' and (resid 151 through 170 )G151 - 170
40X-RAY DIFFRACTION40chain 'G' and (resid 171 through 196 )G171 - 196
41X-RAY DIFFRACTION41chain 'G' and (resid 197 through 216 )G197 - 216
42X-RAY DIFFRACTION42chain 'H' and (resid 10 through 37 )H10 - 37
43X-RAY DIFFRACTION43chain 'H' and (resid 38 through 87 )H38 - 87
44X-RAY DIFFRACTION44chain 'H' and (resid 88 through 102 )H88 - 102
45X-RAY DIFFRACTION45chain 'H' and (resid 103 through 135 )H103 - 135
46X-RAY DIFFRACTION46chain 'H' and (resid 136 through 170 )H136 - 170
47X-RAY DIFFRACTION47chain 'H' and (resid 171 through 216 )H171 - 216

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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://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