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- PDB-2gmw: Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase fro... -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 2gmw
タイトルCrystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli.
要素D,D-heptose 1,7-bisphosphate phosphatase
キーワードHYDROLASE (加水分解酵素) / Zn-binding protein
機能・相同性
機能・相同性情報


D,D-heptose 1,7-bisphosphate phosphatase activity / D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / lipopolysaccharide core region biosynthetic process / magnesium ion binding / zinc ion binding / 細胞質基質
類似検索 - 分子機能
D,D-heptose 1,7-bisphosphate phosphatase / Histidinol-phosphate phosphatase / HAD-superfamily hydrolase,subfamily IIIA / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / ロスマンフォールド / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase
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 / 単波長異常分散 / 解像度: 1.5 Å
データ登録者Zhang, K. / DeLeon, G. / Wright, G.D. / Junop, M.S.
引用ジャーナル: Biochemistry / 年: 2010
タイトル: Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli.
著者: Taylor, P.L. / Sugiman-Marangos, S. / Zhang, K. / Valvano, M.A. / Wright, G.D. / Junop, M.S.
履歴
登録2006年4月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02007年4月10日Provider: repository / タイプ: Initial release
改定 1.12008年5月1日Group: Version format compliance
改定 1.22011年7月13日Group: Version format compliance
改定 1.32017年10月18日Group: Refinement description / カテゴリ: software / Item: _software.name
改定 1.42017年10月25日Group: Author supporting evidence / カテゴリ: pdbx_struct_assembly_auth_evidence
改定 1.52024年2月14日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: D,D-heptose 1,7-bisphosphate phosphatase
B: D,D-heptose 1,7-bisphosphate phosphatase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)47,1124
ポリマ－46,9812
非ポリマー1312
水9,926551
1
A: D,D-heptose 1,7-bisphosphate phosphatase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,5562
ポリマ－23,4911
非ポリマー651
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: D,D-heptose 1,7-bisphosphate phosphatase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)23,5562
ポリマ－23,4911
非ポリマー651
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)51.904, 63.977, 103.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
詳細The biological assembly is a monomer as determined by gel filtration chromatography.

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要素

#1: タンパク質 D,D-heptose 1,7-bisphosphate phosphatase / D-glycero-D-manno-heptose 1 / 7-bisphosphate phosphatase


分子量: 23490.607 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: gmhB / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P63228, 加水分解酵素; エステル加水分解酵素; 1価のリン酸エステル加水分解酵素
#2: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#3: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 551 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 1.82 Å3/Da / 溶媒含有率: 32.6 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.8
詳細: 25% PEG 3350, 0.1M Tris, 0.005M DTT, 0.025M sodium chloride, 11% glyceol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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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: NSLS / ビームライン: X8C / 波長: 1.1 Å
検出器タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2005年10月30日 / 詳細: mirrors
放射モノクロメーター: dual crystal / 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: 1.1 Å / 相対比: 1
反射解像度: 1.5→40.19 Å / Num. all: 54729 / Num. obs: 54729 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / 冗長度: 5.47 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 22.7
反射 シェル解像度: 1.5→1.55 Å / 冗長度: 3.34 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 4.4 / % possible all: 93.1

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解析

ソフトウェア
名称バージョン分類
REFMAC5.2.0005精密化
CrystalClear(MSC/RIGAKU)データ削減
d*TREKデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 1.5→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.828 / SU ML: 0.063 / 交差検証法: THROUGHOUT / σ(F): 1 / ESU R: 0.107 / ESU R Free: 0.085 / 立体化学のターゲット値: Engh & Huber
Rfactor反射数%反射Selection details
Rfree0.21236 2761 5.1 %RANDOM
Rwork0.16274 ---
all0.16529 51887 --
obs0.16529 51887 100 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 23.263 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2---0.87 Å20 Å2
3---1.8 Å2
精密化ステップサイクル: LAST / 解像度: 1.5→25 Å
タンパク質核酸リガンド溶媒全体
原子数3047 0 2 551 3600
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223154
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9494331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6545427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15424.847163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43615542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6971520
X-RAY DIFFRACTIONr_chiral_restr0.0950.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022478
X-RAY DIFFRACTIONr_nbd_refined0.2190.21535
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22175
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2416
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.278
X-RAY DIFFRACTIONr_mcbond_it1.3451.51985
X-RAY DIFFRACTIONr_mcangle_it1.81723137
X-RAY DIFFRACTIONr_scbond_it3.03831330
X-RAY DIFFRACTIONr_scangle_it4.154.51160
LS精密化 シェル解像度: 1.5→1.539 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.307 183 -
Rwork0.213 3517 -
obs--100 %
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)
10.1680.03590.17181.42480.67451.05730.036-0.05830.0648-0.10020.1531-0.0407-0.0081-0.0328-0.1892-0.08470.00990.0051-0.0386-0.0051-0.021520.459349.915217.441
20.760.28560.05471.6782-0.45521.09090.0239-0.0436-0.0111-0.0409-0.0198-0.177-0.0388-0.0366-0.004-0.09540.01440.0004-0.04590.0142-0.03755.77113.008617.5296
31.0191-0.3679-0.02121.15770.44360.92190.0946-0.00390.0988-0.23140.0491-0.016-0.15080.0823-0.1437-0.0378-0.00860.0429-0.0694-0.025-0.00321.997953.822110.2697
41.272-0.08340.03521.00360.03350.79010.04620.0727-0.1267-0.1384-0.0322-0.0930.0321-0.0424-0.014-0.04050.0174-0.0065-0.05520.002-0.06054.7659.438310.0514
50.89590.55120.13531.05190.65530.7550.0517-0.10060.1041-0.27420.1456-0.1406-0.1350.17-0.1972-0.0168-0.00660.0565-0.0252-0.0461-0.01825.062652.07659.9819
61.7467-0.4526-0.32261.6113-0.09120.412-0.01080.0117-0.0091-0.19770.0533-0.1640.0122-0.0934-0.0425-0.03190.0213-0.0035-0.04190.0018-0.07421.692411.23029.6625
70.6567-0.1555-0.23921.22840.52570.94660.0753-0.08490.0269-0.11130.1054-0.0457-0.07590.0664-0.1807-0.0667-0.00480.0167-0.055-0.0296-0.049722.762850.233215.2798
81.3608-0.05740.18720.9737-0.0350.73690.0312-0.0154-0.0437-0.05250.0111-0.0969-0.0196-0.0976-0.0423-0.05830.0153-0.003-0.06710.0007-0.07883.653412.729614.8852
9000000000000000-0.0212-0.0760.08710.0376-0.1025-0.006822.627659.692525.3702
100000000000000000.0019-0.0114-0.04760.00120.0434-0.0153.40992.695124.7372
110.4791-0.64380.00311.47821.07082.06940.0673-0.07190.0815-0.13140.0933-0.1775-0.15690.0498-0.1606-0.0833-0.02130.0283-0.0323-0.0185-0.024524.984652.349916.0423
120.836-0.1112-0.03492.0423-0.15851.1070.0046-0.039-0.0579-0.11560.00430.003-0.0392-0.1047-0.0089-0.05940.0190.0001-0.0418-0.0132-0.07251.550210.609515.5556
130.4994-0.4052-0.02510.51850.68192.3080.1105-0.2490.1657-0.0310.1654-0.1501-0.0770.1623-0.2758-0.0376-0.02790.064-0.0075-0.04060.035421.435453.668222.7919
140.7504-0.9460.0261.3392-0.70593.09230.0532-0.188-0.11520.2014-0.1031-0.08150.1449-0.09480.0499-0.09990.0016-0.0307-0.0080.0207-0.06564.27028.902922.7504
150.1677-0.4389-0.27551.44920.36090.88450.0963-0.08320.1106-0.19810.0583-0.0809-0.08640.1027-0.1547-0.0348-0.01010.0244-0.036-0.0374-0.017924.550750.020510.6517
160.9072-0.79380.14141.81420.28420.81340.050.0059-0.0274-0.1657-0.0471-0.0235-0.0404-0.0584-0.003-0.04640.01730.0027-0.04390.0013-0.08542.124413.174510.5252
170.3781-0.4578-0.09391.28270.46891.08320.1435-0.07240.0553-0.17880.0386-0.088-0.07620.0049-0.1821-0.0425-0.00890.0226-0.0488-0.0158-0.030821.818151.161913.6705
180.5686-0.15890.09821.07050.06461.12960.0313-0.023-0.0567-0.1575-0.0756-0.19920.0149-0.08560.0442-0.04960.00520.0013-0.0510.0083-0.04954.735811.988513.5889
190.5611-0.46760.00251.43390.54320.91130.0924-0.09130.0624-0.17760.03480.0382-0.23920.0133-0.1271-0.028-0.00920.0496-0.0398-0.0395-0.015817.649455.428814.8639
201.3517-0.1878-0.27060.51390.12131.01030.0817-0.0918-0.0744-0.05020.0043-0.07520.00750.0883-0.086-0.020.0122-0.0285-0.0588-0.0034-0.05998.89187.679214.9475
210.6379-0.2372-0.14141.05690.48270.95840.0909-0.12680.02870.00220.0497-0.0426-0.01030.0041-0.1406-0.0635-0.00910.0004-0.0335-0.0167-0.030821.656650.00618.7149
220.8633-0.12020.12381.09550.39640.74820.0888-0.063-0.0352-0.0355-0.0598-0.11710.01420.0127-0.029-0.06260.00980.0014-0.05270.0136-0.06284.501912.981518.3702
231.0373-0.0547-0.31741.34880.38690.1990.1234-0.01970.133-0.32510.2032-0.1436-0.22150.1257-0.32660.01890.01220.0392-0.0098-0.0851-0.000122.044749.43217.8785
240.7715-0.3182-0.49981.60470.51830.390.1210.1333-0.033-0.23360.0202-0.1585-0.10050.05-0.1412-0.01830.01130.0268-0.04080.0353-0.05984.655414.0797.9543
250.771-0.2029-0.50571.11630.75110.82620.0684-0.0920.024-0.10670.1228-0.0276-0.03650.1194-0.1912-0.06030.0047-0.007-0.052-0.0235-0.024323.769246.720513.3071
260.9592-0.19630.3591.30460.10950.99790.0311-0.03690.0198-0.064-0.0247-0.1135-0.043-0.0789-0.0063-0.04940.02350.0038-0.0458-0.001-0.08412.728616.375113.4325
270.6684-0.3998-0.33960.90330.32980.93920.0629-0.17210.0996-0.04180.1815-0.11920.00850.1947-0.2445-0.0584-0.0002-0.0006-0.0312-0.0389-0.018424.88247.466419.7939
281.3424-0.25980.64421.6458-0.20030.5631-0.0257-0.13180.00720.0194-0.0185-0.0075-0.0429-0.1570.0443-0.06010.01540.0171-0.03830.0109-0.091.174515.154319.665
291.0545-0.3474-0.17421.28530.02581.29330.1128-0.09540.042-0.1340.0385-0.02930.00970.0905-0.1513-0.0465-0.01460.0034-0.046-0.0341-0.049824.945147.160112.6986
301.4165-0.5231-0.07361.77650.40941.3090.04780.01380.0609-0.1091-0.0341-0.1108-0.0684-0.0832-0.0137-0.05180.01370-0.06320.0059-0.06671.566915.845112.689
310.608-0.3019-0.14841.6480.49040.90680.0662-0.11060.081-0.01810.10990.03550.06780.1565-0.1761-0.07690.00110.0046-0.0409-0.0157-0.023320.786347.772917.9827
321.95440.21260.00040.5062-0.76012.51580.0831-0.08850.15250.0620.1195-0.1336-0.0098-0.1093-0.2026-0.06540.0204-0.0012-0.0627-0.0187-0.02936.616414.58217.551
331.4996-0.4817-0.06391.98190.05961.52570.118-0.07860.0211-0.11690.02040.1497-0.0838-0.0353-0.1384-0.07880.0021-0.0022-0.0739-0.0082-0.027316.794349.575913.3985
341.6623-1.0339-0.06030.66880.20951.15020.02830.00850.0882-0.05230.0905-0.29150.02030.1051-0.1188-0.04390.00140.0122-0.0467-0.0231-0.02679.769613.490813.7736
351.8624-0.3837-1.66822.6169-2.05533.76190.0291-0.32560.2844-0.03930.0693-0.23760.05060.249-0.0985-0.069-0.00910.05-0.0182-0.10180.01826.367653.181717.8391
361.24370.16291.59272.01292.12863.89060.0345-0.2257-0.15040.0149-0.18170.0535-0.1091-0.14190.1472-0.07520.0287-0.0156-0.01740.0268-0.0864-0.18259.497417.3342
370.7427-0.3732-0.40821.53540.58612.00880.0235-0.20120.01770.07330.1441-0.08490.07120.2058-0.1677-0.0945-0.01760.0054-0.0292-0.0521-0.012521.605948.986822.0068
381.438-0.77931.00791.5627-0.10961.57190.0126-0.10950.05340.12420.0328-0.0450.0566-0.2652-0.0454-0.0338-0.0317-0.0096-0.05130.0017-0.10774.43613.379622.0408
390.6111-0.3847-0.21.42560.44631.293-0.0167-0.0144-0.0306-0.06920.1203-0.0608-0.08140.094-0.1036-0.0644-0.00990.0153-0.0311-0.0315-0.005219.084153.284121.6764
401.9878-0.44580.7171.93420.51520.53490.01980.2007-0.0673-0.2923-0.098-0.1465-0.24130.01420.07820.01990.01560.0042-0.01550.0138-0.06026.523510.150813.9687
414.1766-3.90912.88153.726-2.51222.49510.0628-0.16280.2835-0.21040.1182-0.1410.05210.0145-0.1809-0.01290.0175-0.0156-0.00290.00160.003227.930843.205713.9727
423.6093-2.6084-2.29721.8971.55392.4156-0.2404-0.1314-0.1903-0.0440.0196-0.0443-0.0536-0.02970.2208-0.00860.03780.0228-0.0185-0.036-0.0092-1.094319.921214.3494
430.00610.0072-0.22160.0086-0.26288.07860.15740.0625-0.203-0.2771-0.04360.0848-0.42440.4396-0.1138-0.0138-0.070.08710.0299-0.10050.019222.156159.910724.1419
440.9638-0.3812.10760.1506-0.83314.60890.3378-0.229-0.29850.0894-0.3815-0.14160.2915-0.10280.0437-0.00530.0062-0.0285-0.0170.0384-0.00483.88332.527923.4826
450.28590.2823-0.05440.95450.06260.0876-0.0108-0.0282-0.0113-0.05780.0238-0.05170.00190.0075-0.01290.04220.0178-0.01340.0695-0.00240.018913.802331.151215.5947
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3434
2X-RAY DIFFRACTION1AA4141
3X-RAY DIFFRACTION1AA5454
4X-RAY DIFFRACTION1AA6666
5X-RAY DIFFRACTION1AA7777
6X-RAY DIFFRACTION1AA8181
7X-RAY DIFFRACTION1AA108108
8X-RAY DIFFRACTION1AA118118
9X-RAY DIFFRACTION1AA135135
10X-RAY DIFFRACTION1AA170170
11X-RAY DIFFRACTION1AA178178
12X-RAY DIFFRACTION1AA155155
13X-RAY DIFFRACTION2BB3434
14X-RAY DIFFRACTION2BB4141
15X-RAY DIFFRACTION2BB5454
16X-RAY DIFFRACTION2BB6666
17X-RAY DIFFRACTION2BB7777
18X-RAY DIFFRACTION2BB8181
19X-RAY DIFFRACTION2BB108108
20X-RAY DIFFRACTION2BB118118
21X-RAY DIFFRACTION2BB135135
22X-RAY DIFFRACTION2BB170170
23X-RAY DIFFRACTION2BB178178
24X-RAY DIFFRACTION2BB155155
25X-RAY DIFFRACTION3AA2727
26X-RAY DIFFRACTION3AA5858
27X-RAY DIFFRACTION3AA6868
28X-RAY DIFFRACTION3AA7979
29X-RAY DIFFRACTION3AA8686
30X-RAY DIFFRACTION3AA100100
31X-RAY DIFFRACTION3AA140140
32X-RAY DIFFRACTION3AA149149
33X-RAY DIFFRACTION3AA150150
34X-RAY DIFFRACTION3AA163163
35X-RAY DIFFRACTION3AA164164
36X-RAY DIFFRACTION3AA166166
37X-RAY DIFFRACTION3AA167167
38X-RAY DIFFRACTION3AA179179
39X-RAY DIFFRACTION3AA185185
40X-RAY DIFFRACTION3AA188188
41X-RAY DIFFRACTION3AA189189
42X-RAY DIFFRACTION3AA197197
43X-RAY DIFFRACTION3AA202202
44X-RAY DIFFRACTION4BB2727
45X-RAY DIFFRACTION4BB5858
46X-RAY DIFFRACTION4BB6868
47X-RAY DIFFRACTION4BB7979
48X-RAY DIFFRACTION4BB8686
49X-RAY DIFFRACTION4BB100100
50X-RAY DIFFRACTION4BB140140
51X-RAY DIFFRACTION4BB149149
52X-RAY DIFFRACTION4BB150150
53X-RAY DIFFRACTION4BB163163
54X-RAY DIFFRACTION4BB164164
55X-RAY DIFFRACTION4BB166166
56X-RAY DIFFRACTION4BB167167
57X-RAY DIFFRACTION4BB179179
58X-RAY DIFFRACTION4BB185185
59X-RAY DIFFRACTION4BB188188
60X-RAY DIFFRACTION4BB189189
61X-RAY DIFFRACTION4BB197197
62X-RAY DIFFRACTION4BB202202
63X-RAY DIFFRACTION5AA5959
64X-RAY DIFFRACTION5AA6565
65X-RAY DIFFRACTION5AA9595
66X-RAY DIFFRACTION5AA136136
67X-RAY DIFFRACTION5AA148148
68X-RAY DIFFRACTION5AA153153
69X-RAY DIFFRACTION5AA161161
70X-RAY DIFFRACTION6BB5959
71X-RAY DIFFRACTION6BB6565
72X-RAY DIFFRACTION6BB9595
73X-RAY DIFFRACTION6BB136136
74X-RAY DIFFRACTION6BB148148
75X-RAY DIFFRACTION6BB153153
76X-RAY DIFFRACTION6BB161161
77X-RAY DIFFRACTION7AA24 - 20524 - 205
78X-RAY DIFFRACTION8BB24 - 20724 - 207
79X-RAY DIFFRACTION9AC300
80X-RAY DIFFRACTION10BD300
81X-RAY DIFFRACTION11AA2424
82X-RAY DIFFRACTION11AA7676
83X-RAY DIFFRACTION11AA9898
84X-RAY DIFFRACTION11AA119119
85X-RAY DIFFRACTION11AA139139
86X-RAY DIFFRACTION11AA151151
87X-RAY DIFFRACTION11AA195195
88X-RAY DIFFRACTION12BB2424
89X-RAY DIFFRACTION12BB7676
90X-RAY DIFFRACTION12BB9898
91X-RAY DIFFRACTION12BB119119
92X-RAY DIFFRACTION12BB139139
93X-RAY DIFFRACTION12BB151151
94X-RAY DIFFRACTION12BB195195
95X-RAY DIFFRACTION13AA4040
96X-RAY DIFFRACTION13AA4444
97X-RAY DIFFRACTION13AA114114
98X-RAY DIFFRACTION13AA115115
99X-RAY DIFFRACTION13AA133133
100X-RAY DIFFRACTION13AA145145
101X-RAY DIFFRACTION14BB4040
102X-RAY DIFFRACTION14BB4444
103X-RAY DIFFRACTION14BB114114
104X-RAY DIFFRACTION14BB115115
105X-RAY DIFFRACTION14BB133133
106X-RAY DIFFRACTION14BB145145
107X-RAY DIFFRACTION15AA3030
108X-RAY DIFFRACTION15AA6262
109X-RAY DIFFRACTION15AA6969
110X-RAY DIFFRACTION15AA9191
111X-RAY DIFFRACTION15AA9999
112X-RAY DIFFRACTION15AA106106
113X-RAY DIFFRACTION15AA137137
114X-RAY DIFFRACTION15AA138138
115X-RAY DIFFRACTION15AA144144
116X-RAY DIFFRACTION15AA158158
117X-RAY DIFFRACTION15AA174174
118X-RAY DIFFRACTION15AA193193
119X-RAY DIFFRACTION15AA196196
120X-RAY DIFFRACTION15AA199199
121X-RAY DIFFRACTION16BB3030
122X-RAY DIFFRACTION16BB6262
123X-RAY DIFFRACTION16BB6969
124X-RAY DIFFRACTION16BB9191
125X-RAY DIFFRACTION16BB9999
126X-RAY DIFFRACTION16BB106106
127X-RAY DIFFRACTION16BB137137
128X-RAY DIFFRACTION16BB138138
129X-RAY DIFFRACTION16BB144144
130X-RAY DIFFRACTION16BB158158
131X-RAY DIFFRACTION16BB174174
132X-RAY DIFFRACTION16BB193193
133X-RAY DIFFRACTION16BB196196
134X-RAY DIFFRACTION16BB199199
135X-RAY DIFFRACTION17AA3838
136X-RAY DIFFRACTION17AA4343
137X-RAY DIFFRACTION17AA5555
138X-RAY DIFFRACTION17AA7070
139X-RAY DIFFRACTION17AA7171
140X-RAY DIFFRACTION17AA7272
141X-RAY DIFFRACTION17AA104104
142X-RAY DIFFRACTION17AA120120
143X-RAY DIFFRACTION17AA126126
144X-RAY DIFFRACTION17AA154154
145X-RAY DIFFRACTION17AA165165
146X-RAY DIFFRACTION17AA169169
147X-RAY DIFFRACTION17AA173173
148X-RAY DIFFRACTION17AA175175
149X-RAY DIFFRACTION17AA192192
150X-RAY DIFFRACTION17AA2525
151X-RAY DIFFRACTION18BB2525
152X-RAY DIFFRACTION18BB3838
153X-RAY DIFFRACTION18BB4343
154X-RAY DIFFRACTION18BB5555
155X-RAY DIFFRACTION18BB7070
156X-RAY DIFFRACTION18BB7171
157X-RAY DIFFRACTION18BB7272
158X-RAY DIFFRACTION18BB104104
159X-RAY DIFFRACTION18BB120120
160X-RAY DIFFRACTION18BB126126
161X-RAY DIFFRACTION18BB154154
162X-RAY DIFFRACTION18BB165165
163X-RAY DIFFRACTION18BB169169
164X-RAY DIFFRACTION18BB173173
165X-RAY DIFFRACTION18BB175175
166X-RAY DIFFRACTION18BB192192
167X-RAY DIFFRACTION19AA2626
168X-RAY DIFFRACTION19AA113113
169X-RAY DIFFRACTION19AA116116
170X-RAY DIFFRACTION19AA132132
171X-RAY DIFFRACTION19AA134134
172X-RAY DIFFRACTION19AA180180
173X-RAY DIFFRACTION19AA183183
174X-RAY DIFFRACTION19AA200200
175X-RAY DIFFRACTION20BB2626
176X-RAY DIFFRACTION20BB113113
177X-RAY DIFFRACTION20BB116116
178X-RAY DIFFRACTION20BB132132
179X-RAY DIFFRACTION20BB134134
180X-RAY DIFFRACTION20BB180180
181X-RAY DIFFRACTION20BB183183
182X-RAY DIFFRACTION20BB200200
183X-RAY DIFFRACTION21AA3232
184X-RAY DIFFRACTION21AA6060
185X-RAY DIFFRACTION21AA8080
186X-RAY DIFFRACTION21AA102102
187X-RAY DIFFRACTION21AA124124
188X-RAY DIFFRACTION21AA130130
189X-RAY DIFFRACTION21AA141141
190X-RAY DIFFRACTION21AA176176
191X-RAY DIFFRACTION22BB3232
192X-RAY DIFFRACTION22BB6060
193X-RAY DIFFRACTION22BB8080
194X-RAY DIFFRACTION22BB102102
195X-RAY DIFFRACTION22BB124124
196X-RAY DIFFRACTION22BB130130
197X-RAY DIFFRACTION22BB141141
198X-RAY DIFFRACTION22BB176176
199X-RAY DIFFRACTION23AA6363
200X-RAY DIFFRACTION23AA6464
201X-RAY DIFFRACTION23AA8282
202X-RAY DIFFRACTION23AA131131
203X-RAY DIFFRACTION23AA157157
204X-RAY DIFFRACTION23AA172172
205X-RAY DIFFRACTION23AA204204
206X-RAY DIFFRACTION23AA205205
207X-RAY DIFFRACTION24BB6363
208X-RAY DIFFRACTION24BB6464
209X-RAY DIFFRACTION24BB8282
210X-RAY DIFFRACTION24BB131131
211X-RAY DIFFRACTION24BB157157
212X-RAY DIFFRACTION24BB172172
213X-RAY DIFFRACTION24BB204204
214X-RAY DIFFRACTION24BB205205
215X-RAY DIFFRACTION25AA2828
216X-RAY DIFFRACTION25AA3636
217X-RAY DIFFRACTION25AA4646
218X-RAY DIFFRACTION25AA5252
219X-RAY DIFFRACTION25AA5656
220X-RAY DIFFRACTION25AA7878
221X-RAY DIFFRACTION25AA109109
222X-RAY DIFFRACTION25AA146146
223X-RAY DIFFRACTION25AA181181
224X-RAY DIFFRACTION25AA203203
225X-RAY DIFFRACTION26BB2828
226X-RAY DIFFRACTION26BB3636
227X-RAY DIFFRACTION26BB4646
228X-RAY DIFFRACTION26BB5252
229X-RAY DIFFRACTION26BB5656
230X-RAY DIFFRACTION26BB7878
231X-RAY DIFFRACTION26BB109109
232X-RAY DIFFRACTION26BB146146
233X-RAY DIFFRACTION26BB181181
234X-RAY DIFFRACTION26BB203203
235X-RAY DIFFRACTION27AA2929
236X-RAY DIFFRACTION27AA4949
237X-RAY DIFFRACTION27AA5151
238X-RAY DIFFRACTION27AA6767
239X-RAY DIFFRACTION27AA8383
240X-RAY DIFFRACTION27AA8888
241X-RAY DIFFRACTION27AA123123
242X-RAY DIFFRACTION28BB2929
243X-RAY DIFFRACTION28BB4949
244X-RAY DIFFRACTION28BB5151
245X-RAY DIFFRACTION28BB6767
246X-RAY DIFFRACTION28BB8383
247X-RAY DIFFRACTION28BB8888
248X-RAY DIFFRACTION28BB123123
249X-RAY DIFFRACTION29AA3131
250X-RAY DIFFRACTION29AA3333
251X-RAY DIFFRACTION29AA3939
252X-RAY DIFFRACTION29AA4747
253X-RAY DIFFRACTION29AA5353
254X-RAY DIFFRACTION29AA5757
255X-RAY DIFFRACTION29AA9696
256X-RAY DIFFRACTION29AA101101
257X-RAY DIFFRACTION29AA103103
258X-RAY DIFFRACTION29AA105105
259X-RAY DIFFRACTION29AA107107
260X-RAY DIFFRACTION29AA128128
261X-RAY DIFFRACTION29AA142142
262X-RAY DIFFRACTION29AA147147
263X-RAY DIFFRACTION29AA156156
264X-RAY DIFFRACTION29AA160160
265X-RAY DIFFRACTION29AA190190
266X-RAY DIFFRACTION29AA198198
267X-RAY DIFFRACTION30BB3131
268X-RAY DIFFRACTION30BB3333
269X-RAY DIFFRACTION30BB3939
270X-RAY DIFFRACTION30BB4747
271X-RAY DIFFRACTION30BB5353
272X-RAY DIFFRACTION30BB5757
273X-RAY DIFFRACTION30BB9696
274X-RAY DIFFRACTION30BB101101
275X-RAY DIFFRACTION30BB103103
276X-RAY DIFFRACTION30BB105105
277X-RAY DIFFRACTION30BB107107
278X-RAY DIFFRACTION30BB128128
279X-RAY DIFFRACTION30BB142142
280X-RAY DIFFRACTION30BB147147
281X-RAY DIFFRACTION30BB156156
282X-RAY DIFFRACTION30BB160160
283X-RAY DIFFRACTION30BB190190
284X-RAY DIFFRACTION30BB198198
285X-RAY DIFFRACTION31AA3535
286X-RAY DIFFRACTION31AA7373
287X-RAY DIFFRACTION31AA8484
288X-RAY DIFFRACTION31AA9090
289X-RAY DIFFRACTION31AA9292
290X-RAY DIFFRACTION31AA171171
291X-RAY DIFFRACTION31AA177177
292X-RAY DIFFRACTION31AA182182
293X-RAY DIFFRACTION32BB3535
294X-RAY DIFFRACTION32BB7373
295X-RAY DIFFRACTION32BB8484
296X-RAY DIFFRACTION32BB9090
297X-RAY DIFFRACTION32BB9292
298X-RAY DIFFRACTION32BB171171
299X-RAY DIFFRACTION32BB177177
300X-RAY DIFFRACTION32BB182182
301X-RAY DIFFRACTION33AA3737
302X-RAY DIFFRACTION33AA4848
303X-RAY DIFFRACTION33AA7474
304X-RAY DIFFRACTION33AA168168
305X-RAY DIFFRACTION33AA187187
306X-RAY DIFFRACTION33AA194194
307X-RAY DIFFRACTION34BB3737
308X-RAY DIFFRACTION34BB4848
309X-RAY DIFFRACTION34BB7474
310X-RAY DIFFRACTION34BB168168
311X-RAY DIFFRACTION34BB187187
312X-RAY DIFFRACTION34BB194194
313X-RAY DIFFRACTION35AA4242
314X-RAY DIFFRACTION35AA110110
315X-RAY DIFFRACTION35AA111111
316X-RAY DIFFRACTION35AA143143
317X-RAY DIFFRACTION35AA152152
318X-RAY DIFFRACTION36BB4242
319X-RAY DIFFRACTION36BB110110
320X-RAY DIFFRACTION36BB111111
321X-RAY DIFFRACTION36BB143143
322X-RAY DIFFRACTION36BB152152
323X-RAY DIFFRACTION37AA4545
324X-RAY DIFFRACTION37AA5050
325X-RAY DIFFRACTION37AA6161
326X-RAY DIFFRACTION37AA8585
327X-RAY DIFFRACTION37AA8989
328X-RAY DIFFRACTION37AA9393
329X-RAY DIFFRACTION37AA121121
330X-RAY DIFFRACTION37AA122122
331X-RAY DIFFRACTION37AA159159
332X-RAY DIFFRACTION37AA184184
333X-RAY DIFFRACTION37AA186186
334X-RAY DIFFRACTION38BB4545
335X-RAY DIFFRACTION38BB5050
336X-RAY DIFFRACTION38BB6161
337X-RAY DIFFRACTION38BB8585
338X-RAY DIFFRACTION38BB8989
339X-RAY DIFFRACTION38BB9393
340X-RAY DIFFRACTION38BB121121
341X-RAY DIFFRACTION38BB122122
342X-RAY DIFFRACTION38BB159159
343X-RAY DIFFRACTION38BB184184
344X-RAY DIFFRACTION38BB186186
345X-RAY DIFFRACTION39AA7575
346X-RAY DIFFRACTION39AA8787
347X-RAY DIFFRACTION39AA117117
348X-RAY DIFFRACTION39AA125125
349X-RAY DIFFRACTION39AA162162
350X-RAY DIFFRACTION39AA201201
351X-RAY DIFFRACTION40BB7575
352X-RAY DIFFRACTION40BB8787
353X-RAY DIFFRACTION40BB117117
354X-RAY DIFFRACTION40BB125125
355X-RAY DIFFRACTION40BB162162
356X-RAY DIFFRACTION40BB201201
357X-RAY DIFFRACTION40BB206206
358X-RAY DIFFRACTION40BB207207
359X-RAY DIFFRACTION41AA9494
360X-RAY DIFFRACTION41AA9797
361X-RAY DIFFRACTION41AA191191
362X-RAY DIFFRACTION42BB9494
363X-RAY DIFFRACTION42BB9797
364X-RAY DIFFRACTION42BB191191
365X-RAY DIFFRACTION43AA112112
366X-RAY DIFFRACTION43AA127127
367X-RAY DIFFRACTION43AA129129
368X-RAY DIFFRACTION44BB112112
369X-RAY DIFFRACTION44BB127127
370X-RAY DIFFRACTION44BB129129
371X-RAY DIFFRACTION45A - BE - F301 - 569

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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