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- PDB-5tkf: Neurospora crassa polysaccharide monooxygenase 2 high mannosylation -

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基本情報

登録情報
データベース: PDB / ID: 5tkf
タイトルNeurospora crassa polysaccharide monooxygenase 2 high mannosylation
要素Lytic polysaccharide monooxygenase
キーワードOXIDOREDUCTASE / polysaccharide monooxygenase
機能・相同性
機能・相同性情報


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / extracellular region / metal ion binding
類似検索 - 分子機能
Coagulation Factor XIII; Chain A, domain 1 - #70 / Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61) / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
COPPER (II) ION / OXYGEN MOLECULE / lytic cellulose monooxygenase (C4-dehydrogenating)
類似検索 - 構成要素
生物種Neurospora crassa (菌類)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.1 Å
データ登録者O'Dell, W.B. / Meilleur, F.
資金援助 米国, 1件
組織認可番号国
National Science Foundation (NSF, United States)1069091 米国
引用ジャーナル: Acta Crystallogr F Struct Biol Commun / 年: 2017
タイトル: Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineered Pichia pastoris for X-ray and neutron diffraction.
著者: O'Dell, W.B. / Swartz, P.D. / Weiss, K.L. / Meilleur, F.
履歴
登録2016年10月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年5月17日Provider: repository / タイプ: Initial release
改定 1.12017年9月20日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22019年11月27日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_type.id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年10月4日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
改定 2.22024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Lytic polysaccharide monooxygenase
B: Lytic polysaccharide monooxygenase
C: Lytic polysaccharide monooxygenase
D: Lytic polysaccharide monooxygenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)96,14414
ポリマ－93,1964
非ポリマー2,94810
水18,1591008
1
A: Lytic polysaccharide monooxygenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,5983
ポリマ－23,2991
非ポリマー1,2992
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Lytic polysaccharide monooxygenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,8194
ポリマ－23,2991
非ポリマー5203
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Lytic polysaccharide monooxygenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,1113
ポリマ－23,2991
非ポリマー8122
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Lytic polysaccharide monooxygenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,6164
ポリマ－23,2991
非ポリマー3173
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
A: Lytic polysaccharide monooxygenase
B: Lytic polysaccharide monooxygenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,4177
ポリマ－46,5982
非ポリマー1,8195
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-9 kcal/mol
Surface area17560 Å2
手法PISA
6
C: Lytic polysaccharide monooxygenase
ヘテロ分子

D: Lytic polysaccharide monooxygenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)47,7277
ポリマ－46,5982
非ポリマー1,1295
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area3260 Å2
ΔGint-24 kcal/mol
Surface area17330 Å2
手法PISA
単位格子
Length a, b, c (Å)43.300, 67.040, 84.150
Angle α, β, γ (deg.)97.570, 97.610, 97.430
Int Tables number1
Space group name H-MP1

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要素

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タンパク質 , 1種, 4分子 ABCD

#1: タンパク質
Lytic polysaccharide monooxygenase / Related to cel1 protein


分子量: 23299.104 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Neurospora crassa (菌類) / 遺伝子: G15G9.090, GE21DRAFT_7469 / プラスミド: pPICZalphaA / 発現宿主: Pichia pastoris (菌類) / 株 (発現宿主): X-33 / 参照: UniProt: Q8WZQ2

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糖 , 4種, 4分子

#2: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1235.105 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 多糖 alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 1 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 3種, 1014分子

#5: 化合物
ChemComp-CU / COPPER (II) ION


分子量: 63.546 Da / 分子数: 4 / 由来タイプ: 組換発現 / 式: Cu
#6: 化合物 ChemComp-OXY / OXYGEN MOLECULE / ペルオキシラジカル


分子量: 31.999 Da / 分子数: 2 / 由来タイプ: 合成 / 式: O2
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1008 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.55 Å3/Da / 溶媒含有率: 51.7 %
結晶化温度: 295 K / 手法: 蒸気拡散法 / pH: 6.2 / 詳細: PEG 3350, HEPES

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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: 22-BM / 波長: 1 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2013年12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: 1 Å / 相対比: 1
反射解像度: 2.1→47.97 Å / Num. obs: 52135 / % possible obs: 97.1 % / 冗長度: 2 % / Biso Wilson estimate: 15.99 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.088 / Rrim(I) all: 0.124 / Net I/σ(I): 8.8 / Num. measured all: 102821
反射 シェル解像度: 2.1→2.16 Å / 冗長度: 2 % / Rmerge(I) obs: 0.303 / CC1/2: 0.726 / % possible all: 96.1

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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
Rotation4.36 Å40.31 Å
Translation4.36 Å40.31 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1-2155精密化
MOSFLM7.2.1データ削減
Aimless0.5.27データスケーリング
PHASER2.6.0位相決定
PDB_EXTRACT3.2データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 4EIR

4eir


解像度: 2.1→40.308 Å / SU ML: 0.17 / 交差検証法: FREE R-VALUE / σ(F): 1.67 / 位相誤差: 16.9
Rfactor反射数%反射
Rfree0.1773 1999 3.84 %
Rwork0.1421 --
obs0.1435 52111 97.05 %
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: 87.94 Å2 / Biso mean: 22.1173 Å2 / Biso min: 3.68 Å2
精密化ステップサイクル: final / 解像度: 2.1→40.308 Å
タンパク質核酸リガンド溶媒全体
原子数6544 0 343 1008 7895
Biso mean--46.72 30.34 -
残基数----892
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0037044
X-RAY DIFFRACTIONf_angle_d0.7039674
X-RAY DIFFRACTIONf_chiral_restr0.0481125
X-RAY DIFFRACTIONf_plane_restr0.0041243
X-RAY DIFFRACTIONf_dihedral_angle_d11.1294196
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15250.2191430.17643584372796
2.1525-2.21070.21321400.18133506364696
2.2107-2.27580.23061430.1773597374096
2.2758-2.34920.24181400.16193498363896
2.3492-2.43320.21951430.16133583372697
2.4332-2.53060.20231420.15423562370497
2.5306-2.64570.20121420.1523565370797
2.6457-2.78520.17731440.14483591373597
2.7852-2.95960.18821420.14423585372797
2.9596-3.18810.17961430.14193575371897
3.1881-3.50870.171450.12463624376998
3.5087-4.0160.14131440.11643616376098
4.016-5.05820.13271440.10913608375298
5.0582-40.31590.14791440.15293618376298
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)
11.5666-0.2648-0.18551.1232-1.03991.0553-0.2078-0.31170.14710.31140.1548-0.0058-0.0608-0.1155-0.00780.12530.0512-0.02880.1629-0.05380.16-17.017763.272644.2443
22.50230.1664-0.7181.79110.33111.7105-0.1385-0.273-0.11550.23270.121-0.11720.13950.22760.00480.10530.0370.00020.12840.01050.177-16.888753.956341.1834
36.64623.76284.28442.79951.47924.0288-0.1590.6730.1749-0.34120.2814-0.09850.16960.28120.0810.0955-0.0080.00790.1577-0.07760.163-19.474754.262525.183
41.2959-0.13740.39690.7978-0.15821.4139-0.10070.0716-0.24240.08070.04760.09420.09160.13320.02620.10510.01160.02620.066-0.00030.143-21.870450.373333.3918
52.1045-2.00190.24586.11830.04870.0426-0.4765-0.66770.11190.62040.5924-0.03810.0349-0.0459-0.00540.16140.0766-0.00150.1974-0.00750.1207-27.165363.815749.0268
61.08970.0735-0.76771.05740.36541.3976-0.0454-0.20810.11980.0690.1351-0.0866-0.03230.1756-0.0810.0860.0101-0.03020.1292-0.03470.1591-9.671763.434639.0923
74.70361.8886-0.20352.14460.60124.75870.31420.35850.26890.0141-0.1541-0.298-0.24980.3684-0.14710.110.00160.00490.14480.01690.1922-9.045966.454126.4502
81.51071.0518-1.190.9375-0.62851.0431-0.11490.0692-0.0552-0.12650.0538-0.16740.1046-0.01990.07530.10010.0141-0.02220.0680.01380.1343-26.431365.203432.6937
91.71471.7008-0.28731.72890.00141.8513-0.1254-0.429-0.34670.2314-0.22810.28570.13360.2690.09690.1285-0.00610.07150.15190.05240.3375-36.398254.722343.8138
100.7606-0.05-0.16080.55631.71965.2713-0.2457-0.0189-0.33030.0931-0.02160.25430.1404-0.10950.22910.1170.0089-0.00280.1110.03630.1349-31.399851.693739.1015
111.25350.21450.18720.96550.47481.34510.03040.01810.3148-0.0996-0.0202-0.0571-0.16750.1069-0.0120.08760.01130.0040.08710.02290.1803-20.422271.218230.5433
122.78690.1457-1.12220.6576-0.16021.0315-0.2063-0.15280.2426-0.06030.19150.00820.1350.01840.01310.10890.016-0.00380.1293-0.03870.1605-30.472168.304642.9472
130.80940.2592-0.15091.2965-0.10691.34690.03310.190.07110.01030.0384-0.1581-0.01080.0217-0.03030.09030.0219-0.00340.12210.00290.1303-19.728562.74626.7131
145.10091.03392.1263.93451.16134.0321-0.01880.3340.1372-0.2012-0.0323-0.07980.32710.1083-0.01140.12560.00880.01020.16250.00420.1184-18.423358.052917.5291
150.9714-0.36770.33331.36840.05650.5328-0.0796-0.08510.07730.14660.0637-0.1493-0.0883-0.1256-0.00410.09560.0012-0.00470.09510.0020.079-24.176459.27838.1931
168.0815-2.08833.47534.52780.31825.0832-0.12690.16960.49340.3027-0.0847-0.07880.02510.24890.11390.1016-0.0093-0.01040.1466-0.03040.1358-40.057570.21945.9898
171.03380.4104-0.48630.63790.00490.93230.03260.33240.2280.0224-0.05220.0388-0.0139-0.28660.04830.08140.01680.00260.1745-0.00470.1469-32.156362.133925.3305
184.2126-0.9260.06223.4518-0.56924.2330.31370.35140.1403-0.3839-0.3874-0.2997-0.29910.57280.08990.27050.02560.0430.26960.06830.146-16.187267.717714.7157
194.12950.9251-3.11572.5278-0.61146.83290.17810.19090.2509-0.78990.0105-0.1048-0.4170.1624-0.16240.29170.05680.06520.19570.0560.209-20.661472.809516.9384
202.81440.14220.56951.0987-2.24994.88320.2352-0.16720.6070.1120.0249-0.4811-0.8669-0.6726-0.13880.11820.0150.00830.1448-0.00180.2379-35.079772.391433.4053
211.1858-0.10440.22580.9221-0.84570.77970.110.133-0.669-0.3125-0.18060.41990.1238-0.03170.09660.1164-0.02090.01320.1243-0.0380.1802-7.284137.393721.8079
223.88250.0760.87492.66921.21975.3007-0.01580.3339-0.4071-0.3962-0.0588-0.35030.6813-0.2583-0.02910.28010.03020.08430.1399-0.00170.26-3.6526.282222.1572
232.5329-0.1403-0.46610.42030.84961.7435-0.2294-0.0775-0.4960.46780.0215-0.04530.2957-0.16040.15830.1324-0.0149-0.00860.1090.00650.1848-3.179337.371629.3394
247.35583.8152-3.15272.2127-1.69754.1333-0.07590.09050.49580.28040.310.2145-0.20730.024-0.50710.08880.03060.0210.152-0.05680.1102-8.904849.92725.8083
251.885-0.04860.23281.90140.46171.39280.03920.00180.13260.2031-0.0077-0.15060.05050.0365-0.01890.08610.01050.00720.1153-0.03870.1018-0.530550.812827.2677
263.2519-0.11771.6143.09640.14870.83150.1011-0.0023-0.41920.49680.26610.1910.2079-0.1992-0.330.2690.04610.03060.13010.03140.20233.788230.839327.4875
273.629-0.8725-1.07731.81780.90542.0860.0590.2328-0.51570.1057-0.19-0.00770.2547-0.16970.10770.1574-0.02450.00660.1209-0.04460.1474-3.348733.115317.0279
282.27061.00491.59640.42130.74083.75630.20450.0307-0.16560.0710.0317-0.01770.1945-0.3882-0.24750.1007-0.0339-0.00090.2076-0.010.163-16.757338.012620.7855
290.6207-0.4051-0.60921.786-0.11570.85620.1174-0.0649-0.1513-0.2764-0.0750.05550.2436-0.15710.03370.1043-0.00640.01540.1418-0.02790.0647-5.269145.217413.0515
304.4877-1.0512-1.08056.8324-2.76686.63960.0452-0.4737-0.02680.0081-0.1017-0.444-0.04830.51390.04550.17320.0188-0.0030.17680.02620.177613.840837.982625.0386
311.160.2759-0.88161.32830.0060.6906-0.02370.424-0.065-0.08170.0874-0.02090.02750.0327-0.03210.09880.00530.01520.1551-0.02350.1009-1.138242.899612.9244
321.48170.15020.84441.9551-0.69582.0260.1681.055-0.9317-0.2957-0.19380.14680.2448-0.170.06410.1912-0.00380.01220.1729-0.0740.2137-0.224132.916212.3068
332.6738-0.60670.01331.1477-0.1961.29390.009-0.0269-0.2552-0.0683-0.0046-0.13090.11750.1707-0.01280.13360.0340.00640.1259-0.00810.1367.50337.577218.7747
346.31212.38250.28463.29430.8320.7452-0.07790.37310.6115-0.33570.11660.4078-0.0694-0.1038-0.01980.13860.00760.02440.13290.01770.0841-9.686355.792313.1934
351.16490.5569-0.36380.2617-0.03241.0605-0.01940.0428-0.09080.03390.0182-0.04330.06510.0778-0.01480.1034-0.0052-0.0110.0988-0.03270.11032.637841.990419.7083
363.3634-1.3543-1.28591.04220.05350.91280.25150.4497-0.0307-0.3555-0.2284-0.2881-0.03540.12950.05810.02350.10880.05680.3225-0.07630.166916.101342.798313.0218
371.4527-0.57680.74452.058-0.71770.88390.06710.20630.2966-0.3101-0.0429-0.23760.12940.0727-0.00810.10050.01030.01120.17670.03030.12983.986855.106515.2665
381.62540.28371.88866.01872.51564.8267-0.30710.17280.0967-0.58110.13240.5309-0.7206-0.6126-0.03950.2125-0.0070.01560.33230.08430.1728-9.125357.53468.197
391.14622.56780.03395.7735-0.17163.31180.210.15810.1251-0.34320.2660.8259-0.6257-0.6443-0.18730.68280.2172-0.10630.57650.0670.2841-11.466357.7-0.4787
402.6197-0.04631.36484.2492-0.87082.20970.34890.63530.0058-0.5503-0.1294-0.33790.25840.1952-0.18340.14580.02930.02710.2855-0.00020.11465.557446.00126.7677
411.15980.6279-0.11330.90250.56860.7369-0.0060.0328-0.1618-0.08960.11710.0825-0.0644-0.01210.19730.1396-0.0003-0.04140.0970.05360.1806-27.530424.126648.9676
420.985-1.30032.32611.7093-3.06035.4950.13450.40210.3325-0.15150.25550.2561-0.397-0.37120.70690.26710.0179-0.22430.11020.21050.3044-24.247633.540536.0856
431.0356-0.6241-0.42720.9723-0.82322.3693-0.42010.3431-0.0598-0.49450.29160.29810.3091-0.1531-0.44690.2424-0.0988-0.07470.18970.03910.1168-23.942521.087742.5304
443.7112.14973.1051.4151.55342.9160.2851-0.122-0.18960.2688-0.19340.12420.1453-0.0432-0.1310.14250.017-0.02930.1490.0350.1543-20.984820.129160.4908
451.72380.81731.15672.2961.03321.15090.1325-0.016-0.3124-0.1527-0.0703-0.2995-0.00170.0627-0.05190.1563-0.00980.00120.08730.01560.1638-17.862317.162852.9079
462.12361.5202-0.1211.1571-0.33361.2269-0.32820.32290.0754-0.39680.39040.18180.1156-0.0056-0.01080.2231-0.0271-0.0410.12790.04010.1639-19.206131.482139.4433
470.9732-0.70730.30044.59741.33382.82830.03240.16650.1982-0.2667-0.04240.9670.0577-0.4974-0.07070.1589-0.0345-0.06990.22520.12340.3429-35.819925.294148.4914
481.17290.7035-0.37110.906-0.45881.40610.2230.04290.1220.2521-0.08020.3509-0.279-0.1696-0.14370.19740.01490.03210.078-0.0220.1962-25.415232.073556.6666
495.24140.52681.62517.37962.83284.55040.07270.0828-0.6653-0.51730.0011-0.9450.09420.13810.15850.21720.03240.02820.10950.06130.314-5.768725.957743.2163
500.01720.01820.01250.0707-0.14980.4138-0.14130.0303-0.3611-0.03840.0006-0.35390.45120.3820.11420.27570.01910.0450.15970.02220.2634-9.02720.798446.4662
511.28790.74030.46150.64230.19332.5708-0.0041-0.1414-0.08870.4592-0.1450.3477-0.55430.13350.0720.2735-0.00010.04650.0980.01410.2064-18.670737.436255.7816
520.87580.48930.83671.4671-0.25591.2340.1371-0.07230.18870.1008-0.12060.6208-0.1617-0.35490.05690.1920.07750.08470.1230.04210.4274-31.716936.55656.07
533.01880.5394-0.50581.9315-0.5951.76250.18530.51210.65880.34360.17920.5779-0.2116-0.2383-0.17970.18710.0159-0.00040.12950.08690.2053-23.989136.813745.3292
541.32110.5365-0.84691.5436-0.65571.92940.0360.0268-0.0340.0083-0.06660.01150.04190.2389-0.00040.1409-0.0097-0.02310.09710.01340.1133-13.246132.466346.2623
551.14410.95520.31991.655-0.45120.96230.1187-0.20840.06270.1898-0.18620.1529-0.25810.02440.03760.164-0.0133-0.0150.0714-0.01150.1321-20.828326.698556.021
560.1138-0.06910.26142.595-3.89056.0336-0.1676-0.09810.30470.0688-0.3111-0.1345-0.32930.36040.40740.1742-0.079-0.02380.15960.05170.217-3.406341.024244.2636
571.9790.54890.44321.3217-0.45720.41590.2685-0.2980.26780.3846-0.28970.0434-0.29040.26980.05840.2866-0.1248-0.03190.21410.02990.1762-12.304429.727962.1789
580.69960.4790.65580.44280.11621.64870.0037-0.29460.0710.4397-0.1160.28050.0105-0.31990.32270.5516-0.16160.14090.4148-0.1780.1379-27.717832.521670.9229
590.6413-0.1953-0.11131.63610.12870.7943-0.0712-0.1421-0.08460.61830.10920.24460.1098-0.02370.06681.21230.04190.25390.4096-0.24720.4041-28.927339.940573.0115
602.0202-0.126-0.9440.2740.74433.18950.4468-0.30570.42880.4843-0.19820.0212-0.71880.2834-0.25850.334-0.11940.03540.1817-0.05310.2246-14.329439.479457.2148
611.7880.12820.29955.993-0.74720.76060.18540.115-0.2430.0451-0.3046-0.10610.62820.39120.24860.28570.0460.01110.13050.03340.12955.95266.231564.3802
621.1589-0.87590.69283.3393-0.70440.4281-0.0877-0.2328-0.2150.55310.08810.16130.4609-0.010.03360.71850.11170.17150.15260.03240.28915.756454.68664.5884
632.34210.53720.05222.0416-0.24730.3407-0.46040.1153-0.1258-0.28150.2465-0.07250.6297-0.09940.19440.3049-0.03850.04870.1283-0.03520.13283.600967.470656.2953
648.4217-3.523-4.1281.75792.08532.4620.4136-0.07310.7344-0.2576-0.1512-0.186-0.3703-0.0164-0.07170.17420.0129-0.02450.10550.01590.14371.759581.703362.093
651.5250.2312-0.97890.48330.26532.02570.11780.08310.2465-0.0286-0.0260.1493-0.1175-0.2658-0.0740.14880.0071-0.03680.16560.0220.1278-3.730877.923858.4745
662.75031.58110.18852.71120.93990.39360.13720.0888-0.1631-0.35770.0187-0.1239-0.17440.1774-0.07750.5456-0.06840.10530.1848-0.03910.2353-2.107260.078255.5929
672.9133-0.6685-2.35921.12350.33991.9555-0.56760.0802-0.4392-0.2487-0.04-0.33380.8557-0.16120.41170.6799-0.02510.01490.20330.05410.3064-4.013453.874171.1454
680.6409-0.4540.89930.8611-0.56283.0407-0.0833-0.1405-0.2462-0.0680.0287-0.01460.40350.99650.27020.22280.1429-0.00110.26120.01420.187812.522669.113365.5331
690.8402-0.0502-0.45311.21910.09241.2149-0.07350.0734-0.02330.00070.00260.10510.21440.09130.11010.1886-0.0108-0.02280.1861-0.00380.0793-0.422872.573971.0243
700.9316-1.1935-0.88064.34921.89953.219-0.0690.1473-0.3621-0.4165-0.06090.35040.453-0.7710.05990.301-0.10590.00920.3169-0.01980.164-12.762166.450558.8967
710.4605-0.2002-0.47351.0409-0.13820.6191-0.1849-0.2628-0.11890.19930.1277-0.03610.18880.1630.05550.23390.031-0.01680.233-00.09281.789472.394478.3478
722.87590.13240.22876.0245-0.47820.5356-0.0288-0.4234-0.634-0.01920.054-0.35620.64730.331-0.14660.32890.1876-0.0140.2990.03520.248212.56566.4673.0891
737.79981.27771.19922.12621.40021.4160.0763-1.3129-0.9640.2816-0.37220.00450.63550.03240.18170.3938-0.0033-0.00790.23570.08540.2371-3.98860.334375.0077
743.26631.51650.04543.1070.34511.7814-0.0933-0.1251-0.37090.07420.015-0.03150.4311-0.19430.08840.3076-0.04380.01390.17050.0170.1509-7.340164.209167.0104
754.83390.8485-0.75032.27391.2584.1099-0.1038-0.34560.5246-0.10320.24230.1889-0.47420.2314-0.08630.174-0.025-0.01840.1405-0.00960.14153.987485.92672.4904
761.3877-0.0988-0.75581.0120.00951.8843-0.04150.0561-0.06370.02330.11160.0840.3234-0.0951-0.06360.197-0.0029-0.03350.14290.00670.0992-2.764570.993765.5479
770.82531.6218-0.33026.0143-2.54751.6219-0.1252-0.4532-0.23910.01080.36440.56650.3045-0.4133-0.14170.3195-0.12550.07150.40440.04940.3993-17.81560.382875.4332
781.19310.4114-0.01631.95960.25921.27610.1106-0.10230.17070.2038-0.1290.2904-0.0225-0.48040.0130.17610.00360.020.23570.01560.1579-9.537480.283371.1153
791.81431.61531.2831.4451.3043.19830.0399-0.02310.018-0.00110.092-0.1258-0.29590.6094-0.13940.2601-0.0605-0.0110.2831-0.08070.21615.048788.861381.2646
804.01951.81080.41734.99541.24392.00080.2102-0.18290.07150.6138-0.17680.46550.2123-0.1628-0.05420.2282-0.0070.0530.26440.01380.1235-7.001873.232580.2265
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:15)A1 - 15
2X-RAY DIFFRACTION2(chain A and resid 16:25)A16 - 25
3X-RAY DIFFRACTION3(chain A and resid 26:33)A26 - 33
4X-RAY DIFFRACTION4(chain A and resid 34:48)A34 - 48
5X-RAY DIFFRACTION5(chain A and resid 49:60)A49 - 60
6X-RAY DIFFRACTION6(chain A and resid 61:79)A61 - 79
7X-RAY DIFFRACTION7(chain A and resid 80:85)A80 - 85
8X-RAY DIFFRACTION8(chain A and resid 86:93)A86 - 93
9X-RAY DIFFRACTION9(chain A and resid 94:97)A94 - 97
10X-RAY DIFFRACTION10(chain A and resid 98:105)A98 - 105
11X-RAY DIFFRACTION11(chain A and resid 106:132)A106 - 132
12X-RAY DIFFRACTION12(chain A and resid 133:147)A133 - 147
13X-RAY DIFFRACTION13(chain A and resid 148:160)A148 - 160
14X-RAY DIFFRACTION14(chain A and resid 161:166)A161 - 166
15X-RAY DIFFRACTION15(chain A and resid 167:176)A167 - 176
16X-RAY DIFFRACTION16(chain A and resid 177:183)A177 - 183
17X-RAY DIFFRACTION17(chain A and resid 184:201)A184 - 201
18X-RAY DIFFRACTION18(chain A and resid 202:206)A202 - 206
19X-RAY DIFFRACTION19(chain A and resid 207:217)A207 - 217
20X-RAY DIFFRACTION20(chain A and resid 218:223)A218 - 223
21X-RAY DIFFRACTION21(chain B and resid 1:8)B1 - 8
22X-RAY DIFFRACTION22(chain B and resid 9:16)B9 - 16
23X-RAY DIFFRACTION23(chain B and resid 17:24)B17 - 24
24X-RAY DIFFRACTION24(chain B and resid 25:30)B25 - 30
25X-RAY DIFFRACTION25(chain B and resid 31:46)B31 - 46
26X-RAY DIFFRACTION26(chain B and resid 47:55)B47 - 55
27X-RAY DIFFRACTION27(chain B and resid 56:67)B56 - 67
28X-RAY DIFFRACTION28(chain B and resid 68:81)B68 - 81
29X-RAY DIFFRACTION29(chain B and resid 82:92)B82 - 92
30X-RAY DIFFRACTION30(chain B and resid 93:97)B93 - 97
31X-RAY DIFFRACTION31(chain B and resid 98:130)B98 - 130
32X-RAY DIFFRACTION32(chain B and resid 131:140)B131 - 140
33X-RAY DIFFRACTION33(chain B and resid 141:153)B141 - 153
34X-RAY DIFFRACTION34(chain B and resid 154:161)B154 - 161
35X-RAY DIFFRACTION35(chain B and resid 162:182)B162 - 182
36X-RAY DIFFRACTION36(chain B and resid 183:188)B183 - 188
37X-RAY DIFFRACTION37(chain B and resid 189:200)B189 - 200
38X-RAY DIFFRACTION38(chain B and resid 201:206)B201 - 206
39X-RAY DIFFRACTION39(chain B and resid 207:211)B207 - 211
40X-RAY DIFFRACTION40(chain B and resid 212:223)B212 - 223
41X-RAY DIFFRACTION41(chain C and resid 1:6)C1 - 6
42X-RAY DIFFRACTION42(chain C and resid 7:12)C7 - 12
43X-RAY DIFFRACTION43(chain C and resid 13:25)C13 - 25
44X-RAY DIFFRACTION44(chain C and resid 26:33)C26 - 33
45X-RAY DIFFRACTION45(chain C and resid 34:48)C34 - 48
46X-RAY DIFFRACTION46(chain C and resid 49:65)C49 - 65
47X-RAY DIFFRACTION47(chain C and resid 66:81)C66 - 81
48X-RAY DIFFRACTION48(chain C and resid 82:92)C82 - 92
49X-RAY DIFFRACTION49(chain C and resid 93:97)C93 - 97
50X-RAY DIFFRACTION50(chain C and resid 98:105)C98 - 105
51X-RAY DIFFRACTION51(chain C and resid 106:120)C106 - 120
52X-RAY DIFFRACTION52(chain C and resid 121:129)C121 - 129
53X-RAY DIFFRACTION53(chain C and resid 130:139)C130 - 139
54X-RAY DIFFRACTION54(chain C and resid 140:154)C140 - 154
55X-RAY DIFFRACTION55(chain C and resid 155:178)C155 - 178
56X-RAY DIFFRACTION56(chain C and resid 179:185)C179 - 185
57X-RAY DIFFRACTION57(chain C and resid 186:201)C186 - 201
58X-RAY DIFFRACTION58(chain C and resid 202:206)C202 - 206
59X-RAY DIFFRACTION59(chain C and resid 207:212)C207 - 212
60X-RAY DIFFRACTION60(chain C and resid 213:223)C213 - 223
61X-RAY DIFFRACTION61(chain D and resid 1:9)D1 - 9
62X-RAY DIFFRACTION62(chain D and resid 10:15)D10 - 15
63X-RAY DIFFRACTION63(chain D and resid 16:25)D16 - 25
64X-RAY DIFFRACTION64(chain D and resid 26:31)D26 - 31
65X-RAY DIFFRACTION65(chain D and resid 32:46)D32 - 46
66X-RAY DIFFRACTION66(chain D and resid 47:53)D47 - 53
67X-RAY DIFFRACTION67(chain D and resid 54:60)D54 - 60
68X-RAY DIFFRACTION68(chain D and resid 61:81)D61 - 81
69X-RAY DIFFRACTION69(chain D and resid 82:94)D82 - 94
70X-RAY DIFFRACTION70(chain D and resid 95:107)D95 - 107
71X-RAY DIFFRACTION71(chain D and resid 108:127)D108 - 127
72X-RAY DIFFRACTION72(chain D and resid 128:133)D128 - 133
73X-RAY DIFFRACTION73(chain D and resid 134:141)D134 - 141
74X-RAY DIFFRACTION74(chain D and resid 142:153)D142 - 153
75X-RAY DIFFRACTION75(chain D and resid 154:161)D154 - 161
76X-RAY DIFFRACTION76(chain D and resid 162:179)D162 - 179
77X-RAY DIFFRACTION77(chain D and resid 180:186)D180 - 186
78X-RAY DIFFRACTION78(chain D and resid 187:201)D187 - 201
79X-RAY DIFFRACTION79(chain D and resid 202:210)D202 - 210
80X-RAY DIFFRACTION80(chain D and resid 211:223)D211 - 223

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万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

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