[日本語] English
万見
- PDB-6byu: X-ray crystal structure of Escherichia coli RNA polymerase (RpoB-... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 6byu
タイトルX-ray crystal structure of Escherichia coli RNA polymerase (RpoB-H526Y) and ppApp complex
要素
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
キーワードtransferase/transferase inhibitor / RNA polymerase / ppApp / Escherichia coli X-ray structure / transferase-transferase inhibitor complex
機能・相同性
機能・相同性情報


sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
類似検索 - 分子機能
RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Sigma-70 factors family signature 1. ...RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Gyrase A; domain 2 / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Chem-ECJ / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
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 / 分子置換 / 解像度: 3.6 Å
データ登録者Murakami, K.S. / Molodtsov, V.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087350 米国
引用ジャーナル: Biochim. Biophys. Acta / 年: 2018
タイトル: Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro.
著者: Bruhn-Olszewska, B. / Molodtsov, V. / Sobala, M. / Dylewski, M. / Murakami, K.S. / Cashel, M. / Potrykus, K.
履歴
登録2017年12月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年1月17日Provider: repository / タイプ: Initial release
改定 1.12018年2月14日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22018年8月1日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.32018年8月15日Group: Data collection / Source and taxonomy / Structure summary
カテゴリ: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
改定 2.02018年8月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
カテゴリ: atom_site / entity ...atom_site / entity / entity_src_gen / entity_src_nat / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _entity.src_method / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
改定 2.12020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 2.22023年10月4日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
改定 3.02024年12月25日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id

-
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

-
集合体

登録構造単位
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)921,34020
ポリマ－919,86412
非ポリマー1,4778
水00
1
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)460,67010
ポリマ－459,9326
非ポリマー7384
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area38440 Å2
ΔGint-182 kcal/mol
Surface area150870 Å2
手法PISA
2
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)460,67010
ポリマ－459,9326
非ポリマー7384
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area37880 Å2
ΔGint-179 kcal/mol
Surface area150190 Å2
手法PISA
単位格子
Length a, b, c (Å)186.254, 203.656, 308.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
要素

-
DNA-directed RNA polymerase subunit ... , 4種, 10分子 ABGHCIDJEK

#1: タンパク質
DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


分子量: 36558.680 Da / 分子数: 4 / 変異: H526Y / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli / 株: K12 / 発現宿主: Escherichia coli (strain K12) (大腸菌) / 株 (発現宿主): K12 / 参照: UniProt: P0A7Z4, DNA-directed RNA polymerase
#2: タンパク質 DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


分子量: 150845.906 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli / 株: K12 / 発現宿主: Escherichia coli (strain K12) (大腸菌) / 株 (発現宿主): K12 / 参照: UniProt: P0A8V2, DNA-directed RNA polymerase
#3: タンパク質 DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


分子量: 155366.781 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli / 株: K12 / 発現宿主: Escherichia coli (strain K12) (大腸菌) / 株 (発現宿主): K12 / 参照: UniProt: P0A8T7, DNA-directed RNA polymerase
#4: タンパク質 DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


分子量: 10249.547 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli / 株: K12 / 発現宿主: Escherichia coli (strain K12) (大腸菌) / 株 (発現宿主): K12 / 参照: UniProt: P0A800, DNA-directed RNA polymerase

-
タンパク質 , 1種, 2分子 FL

#5: タンパク質 RNA polymerase sigma factor RpoD / Sigma-70


分子量: 70352.242 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli / 株: K12 / 発現宿主: Escherichia coli (strain K12) (大腸菌) / 株 (発現宿主): K12 / 参照: UniProt: P00579

-
非ポリマー , 3種, 8分子

#6: 化合物 ChemComp-ECJ / (5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate


分子量: 583.129 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H13N5O16P4
#7: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#8: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn

-
詳細

Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.18 Å3/Da / 溶媒含有率: 61.3 %
結晶化温度: 300 K / 手法: 蒸気拡散法
詳細: 0.1 M HEPES-HCl (pH 6.7), 0.2 M MgCl2, 30% PEG400, 10 mM DTT

-
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: CHESS / ビームライン: F1 / 波長: 0.9179 Å
検出器タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2013年3月22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: 0.9179 Å / 相対比: 1
反射解像度: 3.6→30 Å / Num. obs: 135308 / % possible obs: 100 % / 冗長度: 6 % / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.087 / Rrim(I) all: 0.217 / Χ2: 1.237 / Net I/σ(I): 10
反射 シェル解像度: 3.6→3.66 Å / 冗長度: 6 % / Num. unique obs: 6688 / CC1/2: 0.478 / Rpim(I) all: 0.407 / Χ2: 1.171 / % possible all: 100

-
解析

ソフトウェア
名称バージョン分類
PHENIX(1.12_2829)精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5UAQ

5uaq


解像度: 3.6→30 Å / SU ML: 0.6 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 37.29
Rfactor反射数%反射
Rfree0.3113 1979 1.48 %
Rwork0.2439 --
obs0.2449 133683 98.54 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 3.6→30 Å
タンパク質核酸リガンド溶媒全体
原子数54920 0 76 0 54996
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00455829
X-RAY DIFFRACTIONf_angle_d0.77575326
X-RAY DIFFRACTIONf_dihedral_angle_d16.90634557
X-RAY DIFFRACTIONf_chiral_restr0.0468567
X-RAY DIFFRACTIONf_plane_restr0.0059867
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6003-3.69020.39431350.3459016X-RAY DIFFRACTION96
3.6902-3.78980.38831420.37159407X-RAY DIFFRACTION99
3.7898-3.90110.39961390.34589298X-RAY DIFFRACTION98
3.9011-4.02670.39311410.35699115X-RAY DIFFRACTION97
4.0267-4.17030.39991410.329310X-RAY DIFFRACTION98
4.1703-4.33680.35851390.29669359X-RAY DIFFRACTION99
4.3368-4.53350.34071400.27139334X-RAY DIFFRACTION98
4.5335-4.77160.30671400.24439332X-RAY DIFFRACTION98
4.7716-5.06920.29961400.23869368X-RAY DIFFRACTION99
5.0692-5.45850.31491420.23949483X-RAY DIFFRACTION99
5.4585-6.00380.32041440.24669559X-RAY DIFFRACTION100
6.0038-6.86350.35271430.24359577X-RAY DIFFRACTION100
6.8635-8.61330.28541450.20829672X-RAY DIFFRACTION100
8.6133-30.01640.24091480.17749874X-RAY DIFFRACTION99
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)
12.7082.5354-1.29636.5413-1.71863.98060.2597-0.87290.11790.2562-0.24050.2436-0.4880.2246-0.08151.1369-0.03760.06851.1638-0.09310.91066.0845-72.974739.9279
23.52292.9264-1.75587.2314-0.74021.78820.3898-0.80250.12891.5739-0.51210.3523-0.16530.12160.13231.3349-0.04490.22631.1756-0.08450.7732.2953-74.916839.067
30.73790.02560.1712.80613.4368.6952-0.4061-0.55580.25450.46840.3857-0.2423-0.2682-0.4072-0.09211.6670.32120.98250.969-0.56651.6766-26.802-89.013636.4783
49.07342.5210.39123.0760.90366.34410.2415-0.57320.4765-0.5662-0.68972.26681.206-0.30390.40081.2336-0.1251-0.13771.17340.00051.0148-17.8206-90.318630.5899
53.07560.8841-0.38516.05371.92950.9643-0.1813-0.5925-0.45991.38540.18340.30251.5807-0.5465-0.10372.5659-0.40440.72751.65510.36682.1113-26.4512-124.978436.9224
64.0614-0.97820.09412.37021.25624.0402-0.16670.1064-0.4837-0.0523-0.01980.83820.949-0.76590.20361.6382-0.40760.42141.61230.15031.342-16.762-98.682334.6731
71.58040.9284-0.01723.3054-1.65942.39380.12490.23460.23560.3035-0.4426-0.7809-0.56150.85650.22560.8953-0.1353-0.03411.22350.15631.040538.2197-58.918-8.6969
83.0602-1.286-1.1055.41351.51543.27090.13040.0798-1.164-0.9067-0.2947-0.6870.42350.02720.22041.6851-0.11550.33911.3460.11091.558149.3693-93.348-49.6096
94.42571.2178-2.10547.87621.4286.63930.0045-0.20470.4058-0.49740.1642-0.6328-0.77060.1029-0.07441.14180.00420.09411.340.14841.071442.9287-73.5953-36.3178
100.94710.543-0.04812.9840.01542.17780.1053-0.1321-0.0237-0.0646-0.2141-0.30780.32890.49790.08580.4954-0.0531-0.04231.06110.10690.9334.6025-75.4032-1.726
110.78390.3291-0.08421.79010.2521.46870.1161-0.27490.29190.2065-0.0843-0.0847-0.34340.2165-0.00950.8985-0.17570.01920.93560.02790.94419.1964-64.067917.6004
120.8203-0.0883-0.4141.26590.03912.70140.2935-0.2361-0.0275-0.014-0.2150.3931-0.2575-0.3076-0.08850.4676-0.10790.10630.9349-0.08440.9523-8.4166-76.3108-7.1963
131.74580.8946-0.9491.5293-1.58312.3718-0.19720.4182-0.0663-0.5866-0.17860.0087-0.046-0.25680.37810.76920.09130.00821.0456-0.07740.884-4.0467-63.2581-43.9632
141.4538-0.3610.55780.9325-0.1030.90760.22660.2195-0.5047-0.0806-0.20390.21110.49280.0496-0.04380.8251-0.03290.08580.7883-0.05511.0573-3.1504-102.865-10.6286
155.71363.42492.60854.8930.54825.4879-0.3694-1.3071-0.30991.26970.41231.1560.4122-0.7767-0.25361.28270.08020.04981.4121-0.07152.0488-32.317-88.4544-2.9203
164.5721-5.09212.58295.6249-2.71111.5794-0.2925-1.39921.3061-1.20630.375-0.919-0.0023-0.7205-0.1291.51590.18950.19411.4225-0.14262.1646-51.0149-77.416-16.9127
173.3058-3.17022.62978.9849-2.83712.4533-0.07251.88370.9822-0.8219-0.6788-2.8285-1.04410.82050.84211.88570.18210.57791.61580.44161.398816.7484-43.7298-63.7536
181.79581.092-0.43181.74910.92111.9755-0.4825-0.4379-0.0777-0.714-0.13940.4376-0.6014-0.13690.44992.9710.36580.13271.70010.02362.091-4.297-17.2659-67.3539
194.87750.14780.43917.1481-1.05322.11120.5045-0.3524-2.0119-1.7477-0.14311.478-0.9335-2.3551-0.60472.9615-0.406-0.69512.83530.35673.0928-17.9631-43.6855-82.1116
201.6053-0.0108-0.9973.39250.07722.91220.08180.17670.2728-0.7822-0.15-0.1238-0.79250.18480.14371.2626-0.03220.06340.9150.07291.154510.0509-39.1892-45.9612
216.3751-2.4921-1.46735.011.21671.29520.0711-0.91-2.13490.0676-0.35421.4503-0.0121-0.05790.09671.3525-0.0839-0.07491.2521-0.05281.5762-21.4835-53.4706-8.3881
225.4667-0.6406-0.80158.28831.16965.106-0.2811-1.14191.56051.36610.69050.1065-1.29370.0693-0.38291.90.3434-0.08651.453-0.2241.7345-35.6221-38.2458-2.7879
231.59421.00441.22753.95281.50812.24080.0185-0.8735-0.60820.296-0.18350.64260.3097-1.05890.25191.6288-0.0320.62311.57060.31442.2366-109.6403-142.322-32.1597
242.34841.16742.0027.09357.22069.58651.4539-0.79050.13651.9644-0.3275-0.5841.7661-0.2764-1.02951.9191-0.09780.45561.39320.65871.9823-98.1339-152.1453-29.2735
254.33720.0075-1.30144.92215.66677.81210.57510.5585-0.2168-1.236-1.72680.8001-0.1853-0.4841.07811.76340.15220.75221.19670.08111.989-109.6873-122.3498-21.135
263.38751.71331.6913.76884.014.2570.5094-1.0672-0.72821.0011-0.5959-3.55-0.1635-0.2715-0.10732.34510.0433-0.23131.23570.48222.0329-87.1756-125.4419-9.9078
272.97020.84172.83364.1983-2.83476.1199-0.84351.4868-1.21832.02440.41891.2337-0.85380.05630.63131.5968-0.06610.73961.5585-0.32391.9664-95.3004-116.9933-17.7168
283.78471.24630.32798.6756-0.85954.38040.454-0.20650.90550.6034-1.4314.032-1.8904-0.3690.68442.95770.49570.40521.3588-0.19562.5685-95.3576-87.0213-10.424
293.36960.4531.61244.4145-0.96521.10510.5766-1.20670.75910.8487-0.25940.4301-1.6663-0.0349-0.2053.35810.16910.73441.9552-0.51681.9976-87.8033-88.933-2.1718
300.3717-0.26970.02930.95260.71742.3262-1.22120.0809-0.4714-0.01670.58471.85870.11560.14790.30652.75880.20231.00181.5772-0.82082.963-86.3966-78.9013-1.9989
316.7642-3.20991.30583.00351.46853.8917-0.6975-0.966-1.91521.58511.04341.4783-1.47461.2270.10322.31470.02250.77921.6913-0.04941.8201-98.6634-95.9865-12.1822
324.6405-0.91940.10894.41635.29147.04611.80870.46650.7686-0.2208-0.828-2.3262-0.756-0.9243-0.7392.40210.18070.531.45640.11571.547-84.8209-126.2564-17.7269
338.1339-3.15781.06132.52870.7531.128-0.4823-2.09441.4689-0.30370.6256-0.69190.55350.50670.0933.1564-0.0941.01651.6387-0.11871.852-86.6003-115.5716-10.2213
343.23581.19093.97966.1653-2.33897.43531.027-0.19460.902-0.10380.85110.24850.1659-1.9881-1.56711.7560.21770.78452.35070.05241.6718-101.2535-119.1823-7.3535
355.0356-3.2073-2.89273.18481.81713.5468-0.11660.7176-1.1744-0.7246-0.63031.37920.6517-0.23950.70811.931-0.0465-0.11091.0876-0.0631.4206-79.6545-157.0992-80.3516
363.64471.2476-2.35662.6699-1.27143.7246-0.2159-0.1780.32160.15190.0883-0.3685-0.20330.41610.12451.6893-0.0897-0.08451.2707-0.23781.1853-45.7219-129.0623-103.7597
373.63071.4468-3.36153.0961-2.18872.84230.1590.16-0.06480.60950.02690.3651-0.62730.2355-0.18191.84020.0026-0.12291.2052-0.14361.0386-63.7249-144.3305-90.5001
381.8975-1.7466-1.2037.76852.02662.30890.0451-0.0368-0.008-0.85290.02170.352-0.18860.0016-0.03431.4135-0.0884-0.05721.0852-0.00971.1923-80.3913-134.2091-76.0092
390.73550.0995-0.04253.00231.22522.880.0645-0.1471-0.2645-0.09560.09520.46020.0735-0.491-0.19861.5085-0.09050.12981.13020.11041.7006-93.3492-148.7286-53.0009
404.19970.18410.38282.56920.40773.85470.03250.5075-0.4765-0.34030.5460.57470.4296-0.1179-0.36392.512-0.02020.00731.53620.27571.8858-82.7188-170.241-43.4744
412.63421.3884-1.0482.54540.54640.7279-0.41951.0908-0.1916-1.04930.52710.81240.103-0.9209-0.1022.4395-0.1101-0.17471.83710.33781.6323-99.2657-163.2507-61.5309
422.9570.19750.43121.4651-0.15051.6331-0.2755-0.17170.13370.13630.46930.9383-0.3099-0.6933-0.18451.74980.0290.26771.33170.11041.6113-95.9679-127.7314-49.5982
434.9799-1.2987-4.5851.73651.84954.1464-0.3024-1.2037-0.25760.84860.1587-0.2502-0.10561.2633-0.11881.9596-0.20780.06071.1958-0.01421.1483-45.1257-143.7914-34.4132
443.95540.0434-1.9683.22310.13494.74780.2326-0.3187-0.09750.2107-0.2399-0.3567-0.42070.63880.07861.2215-0.0399-0.02951.1262-0.06050.8327-26.6084-155.8911-57.5565
454.4969-1.7866-2.1760.43020.60492.2782-0.35120.1431-0.6650.45730.24350.22210.03410.11490.16392.0084-0.29020.27081.1424-0.1211.4191-60.0383-145.6958-36.9701
461.2077-1.4750.18453.7043-0.1698-0.1645-0.2421-0.41950.34190.57020.33490.11-0.2592-0.1539-0.12722.3237-0.00690.39531.2604-0.21041.2637-72.724-113.8011-29.4698
471.9134-0.15512.15191.13960.76791.3601-0.23130.13790.8507-0.2514-0.06680.0991-1.18310.50390.27162.2469-0.18040.25911.19440.04041.4896-68.2548-105.7826-57.0055
483.8876-0.6961-0.22062.3963-1.43066.1506-0.01490.48710.98080.0666-0.43770.0749-0.98021.21010.34971.9701-0.5254-0.07481.3565-0.00641.4143-36.9075-107.677-51.6027
492.8384-2.0077-2.03075.27920.7421.61740.1199-0.32130.54260.5412-0.006-0.7407-0.62561.0834-0.01811.6649-0.3312-0.08681.241-0.20141.3139-34.3632-131.9038-42.4803
503.90813.16434.76389.42562.48856.27520.8456-0.3397-1.56470.70740.70180.04981.05120.2341-0.95383.9385-0.6307-1.58631.65210.33362.2512-61.0931-122.5654-18.4942
511.87-2.7912-0.07275.44543.10937.1483-2.1999-2.6427-1.99192.48941.47891.76760.31990.7740.90673.20860.02860.52662.62910.45432.3227-48.8858-126.5341-17.445
526.4761-1.7447-0.30313.60083.23943.1669-1.7717-1.99331.58735.19040.8006-0.03340.34891.711.10213.08570.1277-0.34712.8833-0.41082.4735-57.0967-133.9144-7.3113
532.4459-2.0608-0.19934.56891.41585.3877-0.0676-1.20772.0328-0.5168-0.7553-2.45491.36710.78390.48373.7051.31290.34013.9533-0.73092.9985-53.3288-126.2267-11.2984
542.30951.9275-1.75072.9216-0.9023.20530.13960.64110.444-0.21011.49251.22610.63340.483-1.90663.9714-0.3008-1.03072.91110.35842.8079-36.976-134.6852-3.1115
552.8807-2.46730.55363.50341.45362.56330.38581.1701-1.1405-1.1874-0.72090.59580.36560.2750.55942.81680.10240.58351.9054-0.15231.9051-21.5272-174.0458-84.3483
565.2608-4.54660.19643.66790.0034.69440.5239-0.8840.4736-0.17950.36890.0183-0.626-0.0904-0.92552.9469-0.21270.6581.81060.14242.2559-6.384-196.1469-67.1621
573.65183.77571.02436.15840.35842.1654-0.25490.6153-2.1265-0.8589-1.2168-2.14520.0871-1.3271.32592.7506-0.02350.10023.3108-0.30963.832719.1692-171.5585-61.1205
584.9169-2.8517-1.07253.16370.70722.4816-0.1338-0.4247-0.7892-0.4779-0.3130.0247-0.050.60140.36872.2313-0.19050.20831.42490.10911.4345-20.5019-179.0077-74.0831
593.16950.43232.73632.90410.17623.44560.10780.8899-0.30940.19910.33520.88030.739-0.2247-0.22551.7853-0.15880.27241.546-0.09171.6876-59.8563-177.6837-64.376
602.3073-0.4893-0.25020.4805-1.88068.93590.4178-0.23520.2810.2935-0.2122-0.0341-1.86610.9107-0.05482.2257-0.3305-0.02020.9995-0.01691.3545-52.908-163.2556-23.4181
617.3720.4312-1.5386.5771-0.39257.0837-0.52570.0899-0.66521.09340.2131-0.07391.55570.37110.30272.0135-0.21810.14071.42690.09071.9049-51.3801-177.4228-9.2228
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:119 )A7 - 119
2X-RAY DIFFRACTION2( CHAIN A AND RESID 120:232 )A120 - 232
3X-RAY DIFFRACTION3( CHAIN A AND RESID 233:234 )A233 - 234
4X-RAY DIFFRACTION4( CHAIN B AND RESID 6:49 )B6 - 49
5X-RAY DIFFRACTION5( CHAIN B AND RESID 50:150 )B50 - 150
6X-RAY DIFFRACTION6( CHAIN B AND RESID 151:233 )B151 - 233
7X-RAY DIFFRACTION7( CHAIN C AND RESID 3:158 )C3 - 158
8X-RAY DIFFRACTION8( CHAIN C AND RESID 159:358 )C159 - 358
9X-RAY DIFFRACTION9( CHAIN C AND RESID 359:437 )C359 - 437
10X-RAY DIFFRACTION10( CHAIN C AND RESID 438:767 )C438 - 767
11X-RAY DIFFRACTION11( CHAIN C AND RESID 768:1210 )C768 - 1210
12X-RAY DIFFRACTION12( CHAIN C AND RESID 1211:1342 )C1211 - 1342
13X-RAY DIFFRACTION13( CHAIN D AND RESID 8:354 )D8 - 354
14X-RAY DIFFRACTION14( CHAIN D AND RESID 355:1376 )D355 - 1376
15X-RAY DIFFRACTION15( CHAIN E AND RESID 2:60 )E2 - 60
16X-RAY DIFFRACTION16( CHAIN E AND RESID 61:90 )E61 - 90
17X-RAY DIFFRACTION17( CHAIN F AND RESID 95:135 )F95 - 135
18X-RAY DIFFRACTION18( CHAIN F AND RESID 136:262 )F136 - 262
19X-RAY DIFFRACTION19( CHAIN F AND RESID 263:333 )F263 - 333
20X-RAY DIFFRACTION20( CHAIN F AND RESID 334:510 )F334 - 510
21X-RAY DIFFRACTION21( CHAIN F AND RESID 511:562 )F511 - 562
22X-RAY DIFFRACTION22( CHAIN F AND RESID 563:612 )F563 - 612
23X-RAY DIFFRACTION23( CHAIN G AND RESID 8:138 )G8 - 138
24X-RAY DIFFRACTION24( CHAIN G AND RESID 139:179 )G139 - 179
25X-RAY DIFFRACTION25( CHAIN G AND RESID 180:231 )G180 - 231
26X-RAY DIFFRACTION26( CHAIN H AND RESID 6:34 )H6 - 34
27X-RAY DIFFRACTION27( CHAIN H AND RESID 35:49 )H35 - 49
28X-RAY DIFFRACTION28( CHAIN H AND RESID 50:69 )H50 - 69
29X-RAY DIFFRACTION29( CHAIN H AND RESID 70:133 )H70 - 133
30X-RAY DIFFRACTION30( CHAIN H AND RESID 134:145 )H134 - 145
31X-RAY DIFFRACTION31( CHAIN H AND RESID 146:179 )H146 - 179
32X-RAY DIFFRACTION32( CHAIN H AND RESID 180:197 )H180 - 197
33X-RAY DIFFRACTION33( CHAIN H AND RESID 198:212 )H198 - 212
34X-RAY DIFFRACTION34( CHAIN H AND RESID 213:234 )H213 - 234
35X-RAY DIFFRACTION35( CHAIN I AND RESID 3:158 )I3 - 158
36X-RAY DIFFRACTION36( CHAIN I AND RESID 159:408 )I159 - 408
37X-RAY DIFFRACTION37( CHAIN I AND RESID 409:481 )I409 - 481
38X-RAY DIFFRACTION38( CHAIN I AND RESID 482:688 )I482 - 688
39X-RAY DIFFRACTION39( CHAIN I AND RESID 689:863 )I689 - 863
40X-RAY DIFFRACTION40( CHAIN I AND RESID 864:979 )I864 - 979
41X-RAY DIFFRACTION41( CHAIN I AND RESID 980:1084 )I980 - 1084
42X-RAY DIFFRACTION42( CHAIN I AND RESID 1085:1271 )I1085 - 1271
43X-RAY DIFFRACTION43( CHAIN I AND RESID 1272:1342 )I1272 - 1342
44X-RAY DIFFRACTION44( CHAIN J AND RESID 16:307 )J16 - 307
45X-RAY DIFFRACTION45( CHAIN J AND RESID 308:405 )J308 - 405
46X-RAY DIFFRACTION46( CHAIN J AND RESID 406:649 )J406 - 649
47X-RAY DIFFRACTION47( CHAIN J AND RESID 650:854 )J650 - 854
48X-RAY DIFFRACTION48( CHAIN J AND RESID 855:1301 )J855 - 1301
49X-RAY DIFFRACTION49( CHAIN J AND RESID 1302:1375 )J1302 - 1375
50X-RAY DIFFRACTION50( CHAIN K AND RESID 2:6 )K2 - 6
51X-RAY DIFFRACTION51( CHAIN K AND RESID 7:31 )K7 - 31
52X-RAY DIFFRACTION52( CHAIN K AND RESID 32:45 )K32 - 45
53X-RAY DIFFRACTION53( CHAIN K AND RESID 46:60 )K46 - 60
54X-RAY DIFFRACTION54( CHAIN K AND RESID 61:80 )K61 - 80
55X-RAY DIFFRACTION55( CHAIN L AND RESID 94:135 )L94 - 135
56X-RAY DIFFRACTION56( CHAIN L AND RESID 136:292 )L136 - 292
57X-RAY DIFFRACTION57( CHAIN L AND RESID 293:333 )L293 - 333
58X-RAY DIFFRACTION58( CHAIN L AND RESID 334:446 )L334 - 446
59X-RAY DIFFRACTION59( CHAIN L AND RESID 447:510 )L447 - 510
60X-RAY DIFFRACTION60( CHAIN L AND RESID 511:562 )L511 - 562
61X-RAY DIFFRACTION61( CHAIN L AND RESID 563:613 )L563 - 613

+
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