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- PDB-5tvl: Crystal structure of foldase protein PrsA from Streptococcus pneu... -

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基本情報

登録情報
データベース: PDB / ID: 5tvl
タイトルCrystal structure of foldase protein PrsA from Streptococcus pneumoniae str. Canada MDR_19A
要素Foldase protein PrsA
キーワードISOMERASE / foldase prsA surface-exposed protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
機能・相同性
機能・相同性情報


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / plasma membrane
類似検索 - 分子機能
PPIC-type PPIASE domain / Foldase protein PrsA / Trigger factor/SurA domain superfamily / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Prokaryotic membrane lipoprotein lipid attachment site profile.
類似検索 - ドメイン・相同性
Foldase protein PrsA
類似検索 - 構成要素
生物種Streptococcus pneumoniae (肺炎レンサ球菌)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.55 Å
データ登録者Borek, D. / Yim, V. / Kudritska, M. / Wawrzak, Z. / Stogios, P.J. / Otwinowski, Z. / Savchenko, A. / Anderson, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
引用ジャーナル: To Be Published
タイトル: Crystal structure of foldase protein PrsA from Streptococcus pneumoniae str. Canada MDR_19A
著者: Center for Structural Genomics of Infectious Diseases (CSGID)
履歴
登録2016年11月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年11月23日Provider: repository / タイプ: Initial release
改定 1.12016年11月30日Group: Structure summary
改定 2.02021年2月17日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_sheet_range / 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_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
改定 2.12024年3月6日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Foldase protein PrsA
B: Foldase protein PrsA
C: Foldase protein PrsA
D: Foldase protein PrsA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)128,74221
ポリマ-127,5614
非ポリマー1,18117
1,63991
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint-176 kcal/mol
Surface area56740 Å2
手法PISA
単位格子
Length a, b, c (Å)72.315, 70.940, 116.626
Angle α, β, γ (deg.)90.00, 91.49, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Foldase protein PrsA


分子量: 31890.312 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Streptococcus pneumoniae (肺炎レンサ球菌)
: Canada MDR_19A / 遺伝子: prsA, SPH_1082 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): CodonPlus(DE3)-RIL / 参照: UniProt: B1IBE1, peptidylprolyl isomerase
#2: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 7 / 由来タイプ: 合成 / : Cl
#3: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 3 / 由来タイプ: 合成 / : SO4
#4: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 7 / 由来タイプ: 合成 / : C3H8O3
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 91 / 由来タイプ: 天然 / : 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: 2.34 Å3/Da / 溶媒含有率: 47.53 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 11 / 詳細: 2M Ammonium Sulfate, 0.05 M CAPSO pH 11

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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: 21-ID-F / 波長: 0.97872 Å
検出器タイプ: RAYONIX MX-225 / 検出器: CCD / 日付: 2012年10月7日
放射モノクロメーター: C(111) / 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: 2.45→50 Å / Num. obs: 43458 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 9.8 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 20.04
反射 シェル解像度: 2.45→2.49 Å / 冗長度: 6.2 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.58 / % possible all: 90.9

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0135精密化
HKL-3000データ削減
HKL-3000データスケーリング
HKL-3000位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.55→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.854 / SU B: 31.841 / SU ML: 0.331 / 交差検証法: THROUGHOUT / ESU R Free: 0.439 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.29708 1646 5.2 %RANDOM
Rwork0.22527 ---
obs0.22879 30311 82.35 %-
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
原子変位パラメータBiso mean: 56.404 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.11 Å2
2--0.19 Å2-0 Å2
3----0.3 Å2
精密化ステップサイクル: 1 / 解像度: 2.55→50 Å
タンパク質核酸リガンド溶媒全体
原子数8456 0 64 91 8611
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0070.028635
X-RAY DIFFRACTIONr_bond_other_d0.0010.028367
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.96711612
X-RAY DIFFRACTIONr_angle_other_deg0.797319374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.08951066
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26727.19420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.998151697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7241516
X-RAY DIFFRACTIONr_chiral_restr0.0520.21345
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021764
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.872.564282
X-RAY DIFFRACTIONr_mcbond_other2.8692.5594281
X-RAY DIFFRACTIONr_mcangle_it4.663.8235342
X-RAY DIFFRACTIONr_mcangle_other4.6593.8245343
X-RAY DIFFRACTIONr_scbond_it3.4132.8484353
X-RAY DIFFRACTIONr_scbond_other3.4132.8484353
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4214.1316271
X-RAY DIFFRACTIONr_long_range_B_refined7.52719.3419349
X-RAY DIFFRACTIONr_long_range_B_other7.52619.3439348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 2.55→2.616 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.397 67 -
Rwork0.322 1021 -
obs--38.19 %
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.00081.93046.02593.00936.542418.5039-0.42581.41640.1591-0.18540.3240.5052-0.84121.37660.10190.1487-0.149-0.03290.59960.00830.475569.5317.051-43.953
22.69211.5198-0.95681.2858-0.537.4631-0.13710.24470.2064-0.04150.00860.1295-0.3119-0.01930.12840.2051-0.0281-0.05660.23140.01290.153263.06211.105-28.632
37.51691.29889.15642.1632-1.118314.93230.00790.40040.14190.1359-0.154-0.0002-0.22720.80540.1460.2515-0.01860.08070.266-0.050.293173.00210.987-6.25
413.84143.74687.766819.45287.05167.0294-0.0962-0.30240.23210.6950.3343-0.85190.15860.2538-0.23810.20160.0429-0.05190.23280.03850.224175.553-6.435-6.87
513.81590.90122.96678.38891.89496.4172-0.23670.5244-0.292-0.24250.0766-0.7220.10480.68650.16020.1366-0.0177-0.0040.2438-0.03190.220669.101-13.049-16.891
60.03740.03840.28193.89283.52019.1792-0.00560.03310.0789-0.2161-0.02720.01710.03510.40580.03270.1671-0.0729-0.01070.2960.00310.23670.3420.11-13.336
72.16590.7074-4.79910.7379-1.717710.70660.2268-0.091-0.0422-0.0542-0.23870.1901-0.52160.21570.0120.2377-0.0001-0.01760.5468-0.12280.1760.7898.73311.26
82.97611.0288-3.07112.90340.94525.3856-0.1936-0.59340.22820.26470.21180.48970.79620.9229-0.01820.32720.2461-0.02850.46130.00790.105452.377-17.0415.746
94.48966.11476.24948.99365.303724.28070.3352-0.1527-0.35760.3208-0.0869-0.52480.9551-0.702-0.24830.70720.04380.1570.21530.1310.327243.988-32.79214.311
108.627814.78437.623825.336813.06456.73740.33330.4715-1.26230.52490.7894-2.17260.28440.398-1.12280.78530.32210.11410.46590.11950.277850.066-32.5321.84
111.0517-3.84620.082732.8148-5.96361.7220.00050.3156-0.22670.0432-0.4716-0.909-0.0405-0.22820.4710.40130.40660.00030.68040.09130.554157.046-33.83616.416
122.51622.1586-1.69932.0091-1.5771.2385-0.33060.116-0.563-0.132-0.002-0.43040.11590.00940.33260.51720.40530.05270.909-0.14760.277759.993-26.23112.385
134.1005-1.08240.39592.79571.43381.0126-0.3794-0.00970.28270.15690.3094-0.0070.09080.2510.070.3710.1280.02270.3779-0.01020.053749.808-16.29915.398
144.49061.0518-1.30090.74022.694118.7282-0.21490.5650.1776-0.12550.29790.0489-0.56320.732-0.0830.31610.02780.04120.26220.04090.258548.15-21.653.62
1552.36254.83896.72750.50650.64840.91920.6825-1.6672-1.2272-0.0564-0.3801-0.14170.1718-0.2921-0.30240.86690.5692-0.41550.93960.06180.448254.392-21.10323.661
160.6282.34061.439310.87934.63633.5460.00480.06760.02020.629-0.1541-0.2066-0.190.30810.14930.25680.0156-0.01570.54070.04170.190760.23-2.15125.855
175.8573-3.49176.62633.9746-9.487323.7071-0.2775-0.27330.3716-0.23340.0828-0.13330.8557-0.10090.19460.2339-0.095-0.00080.40770.01970.160560.3091.88310.503
185.22267.7142-4.543114.4379-2.42239.9976-0.0038-0.09180.2353-0.0738-0.12370.5838-0.06970.09230.12760.16720.0061-0.02380.2774-0.02430.195857.7518.772-1.899
190.8019-1.9908-1.1935.94424.10463.0842-0.0903-0.07950.2972-0.3248-0.0561-0.2093-0.5249-0.14260.14640.53170.0154-0.18690.2763-0.16240.528163.32921.064-13.007
2012.18850.4056-1.58381.2133-1.46671.8722-0.2165-0.20150.3210.59130.29520.0408-0.6763-0.3317-0.07860.40460.02950.00230.2973-0.08680.37357.03416.562-15.983
2112.71291.2882-1.77350.1586-0.075522.6872-0.125-0.4362-0.31570.0755-0.0314-0.0843-0.40130.05390.15630.35460.0601-0.09460.23030.02540.228933.153.10645.662
221.1836-0.56320.34881.47850.08333.7533-0.0048-0.08580.3384-0.02420.0176-0.0692-0.15280.1966-0.01270.1990.0344-0.02170.2979-0.02850.168139.9198.24529.085
2311.22193.2193.92524.9675.725810.0250.1218-0.23050.1837-0.149-0.07670.24350.0539-0.5195-0.04510.23520.0111-0.03050.18610.0320.114531.3378.0517.012
2424.8022-1.115611.56310.0566-0.51295.4735-0.3294-0.25740.086-0.00450.07860.0007-0.2935-0.09980.25090.4404-0.1103-0.27080.7352-0.1040.594828.606-4.8042.705
258.3119-5.5165.502210.1749-2.22674.06110.60050.0521-0.1609-0.7762-0.61710.34490.4711-0.06180.01670.36640.0270.02550.3157-0.09050.174336.443-13.8368.889
266.954.40361.714.35573.61476.90780.0812-1.2604-0.03160.4011-0.51540.13180.0716-0.58680.43430.28990.16220.04250.5286-0.03420.106139.411-14.04320.545
275.4832-2.6023-2.230312.3503-10.033913.7074-0.2556-0.1540.03950.14550.16850.17670.193-0.16560.08710.1484-0.00590.01190.1787-0.06850.158133.756-3.78613.425
283.21623.165-8.72185.2262-10.5125.4699-0.01790.3658-0.2655-0.1554-0.4494-0.08730.0948-0.26130.46720.2534-0.00610.05590.384-0.05760.211939.9377.102-3.664
293.4963-6.62441.521812.6333-2.8991.07250.82510.41780.2812-1.5994-0.8887-0.5891-0.12190.11020.06360.82570.18360.13230.35730.0760.26150.913.853-18.12
304.0454-1.8098-0.27393.9243-0.28851.1277-0.1957-0.1739-0.22020.0410.1835-0.12480.1570.08480.01230.14440.03180.00110.28770.02870.175860.383-23.978-13.12
315.9812.8297-4.24442.3964-3.48177.5897-0.1711-0.2248-1.1634-0.3529-0.1578-0.14050.43910.39530.32890.26620.0395-0.01950.1548-0.01040.41959.593-31.439-16.654
3210.6915-4.5632-0.60319.3979-7.22757.5644-0.2916-0.2486-0.5745-0.62790.21150.20720.741-0.1470.080.3227-0.0408-0.07660.55740.02180.277349.503-27.19-12.143
335.0722-1.39040.06142.06690.67431.852-0.13570.10030.1522-0.01480.0736-0.05570.1827-0.11120.06220.2296-0.00230.00210.24220.02330.131457.822-15.445-16.338
346.4498-3.19834.84112.381-0.97389.1009-0.1393-0.062-0.178-0.06080.2153-0.107-0.2780.0725-0.07610.1949-0.02120.02640.17650.02310.193758.288-18.968-14.088
352.01233.8659-1.55927.4321-2.99661.2084-0.38240.23910.0866-0.78210.45480.18820.3047-0.1889-0.07230.67740.3755-0.11940.83990.21730.188645.382-0.96-25.189
364.6098-1.05198.525219.20473.807617.5521-0.2422-0.3597-0.106-0.07510.36810.2553-0.4297-0.7108-0.12580.177-0.0960.05270.53090.04620.182243.768-0.198-13.845
375.67553.48328.18312.578311.385221.02250.30180.2876-0.5012-0.02960.1033-0.62450.5505-0.0428-0.40510.21630.03240.09860.278-0.02230.219847.9312.836-1.742
384.4179-6.2738-5.193911.91537.836.2480.1161-0.12020.3669-0.19750.1328-0.0506-0.24720.2535-0.2490.2981-0.0946-0.14050.30660.10290.345243.78711.1194.702
392.3712-0.5266-1.41832.49-2.299911.96910.19160.04590.46850.321-0.1044-0.1254-1.10730.0999-0.08720.2351-0.0156-0.00510.1636-0.03760.367539.17318.94517.439
404.80542.8852-3.63556.69181.38778.83950.1528-0.15910.195-0.066-0.0087-0.4438-0.72521.1577-0.14410.1636-0.0867-0.11520.38590.05040.541345.79514.77417.371
411.5124-2.07432.26573.2458-3.52116.06390.00180.0746-0.03390.02890.06350.04860.0034-0.2037-0.06520.18630.0198-0.01530.2832-0.01010.148835.4016.68427.298
425.98922.86983.99343.41921.5187.23590.169-0.18340.0851-0.0337-0.092-0.0778-0.4934-0.4162-0.07690.19120.0287-0.00840.1893-0.0040.151446.1662.67151.418
4313.42995.9383-8.43253.48180.312825.01780.6073-0.56420.27750.4347-0.18570.00740.06050.9265-0.42160.3231-0.0857-0.19050.21940.04290.281560.6899.92547.322
4421.80660.062215.78960.4628-3.19434.12740.17760.5798-1.06640.3203-0.1216-0.114-2.13181.2983-0.05590.2669-0.10650.00250.3688-0.10410.31966.89211.46335.294
455.78211.8938-5.31943.8478-5.912117.17440.2790.73930.08940.17220.09040.3198-0.73040.1855-0.36930.18550.002-0.03790.31030.00110.174756.2439.88634.067
461.09960.65391.53822.6630.04572.61360.0724-0.0119-0.05550.0330.09310.0713-0.04070.0853-0.16550.2334-0.02040.03940.4351-0.04820.159254.374-3.5254.066
471.3606-0.5069-1.830.3882-0.3968.4517-0.4029-0.1569-0.55940.24520.13670.25390.1824-0.12550.26630.35270.0754-0.07080.29140.03550.629464.734-19.19261.92
482.8251.9346-2.51764.9842-4.65014.6472-0.0756-0.3421-0.27210.17160.02390.1159-0.2448-0.00940.05170.30210.2178-0.06560.4086-0.03080.271480.688-8.83149.752
492.76381.9661-3.67912.0678-5.070313.95280.0760.62430.1471-0.17630.10520.11680.5890.4803-0.18120.65890.12-0.15870.52350.06920.072585.94-5.90230.559
508.72020.04435.439510.44853.18194.35372.5625-0.1516-0.8887-2.8284-1.9116-0.51560.7353-0.628-0.65091.53540.403-0.14360.91930.35820.588196.374-11.55336.327
511.795-2.4802-3.115511.29132.23236.13380.2428-0.34430.2249-0.6259-0.0776-0.3626-0.52040.6995-0.16510.2601-0.0037-0.07680.2318-0.11820.483490.583-0.34140.831
521.1037-2.60763.88086.7558-9.26213.7507-0.2750.12940.05960.9930.01480.0425-1.17680.50570.26030.537-0.0241-0.02830.33390.06480.667385.445-0.15548.93
537.30464.24494.83849.38791.04625.92290.4274-0.25680.4298-0.14250.01511.2858-0.5643-1.4789-0.44260.13790.1339-0.03940.40460.06980.469473.629-6.55750.599
540.02980.16670.30282.95595.612510.82090.0908-0.0301-0.03710.0096-0.2480.0166-0.0334-0.75810.15720.3971-0.0845-0.15670.73550.03620.437176.135-12.30445.406
550.5571-0.00431.40860.0505-0.41037.23440.2139-0.0449-0.1778-0.03350.09490.00310.6378-0.6877-0.30880.3640.0449-0.35860.3752-0.1260.378382.69-13.43742.561
560.8114-0.7548-1.15841.9516-0.54634.00890.06130.1326-0.1222-0.296-0.15280.07920.1844-0.36540.09160.2173-0.0284-0.12460.3860.05560.267282.138-10.98849.213
570.4180.3582.18652.90272.909312.2887-0.0806-0.06340.12180.02-0.1115-0.573-0.2305-0.06010.19210.13220.2406-0.05480.5071-0.05510.372468.064-11.03962.182
5813.9477-2.902-0.99331.3499-1.27043.00450.01310.2728-0.1424-0.0876-0.0924-0.01370.18830.09150.07930.21750.0008-0.00540.2381-0.04930.217550.217-10.04449.388
594.81891.81393.56721.9439-5.295537.60060.2167-0.39070.6996-0.2650.15250.43872.0264-1.8086-0.36930.2928-0.01090.07030.32590.04340.271831.639-3.93141.383
600.47291.72981.10756.37444.08072.61280.046-0.0255-0.020.1556-0.10640.10070.1127-0.0790.06030.505-0.1983-0.09350.4223-0.01130.640738.848-8.8239.242
613.24950.19812.44311.60423.32818.3126-0.5850.43960.2335-0.09050.38310.0791-0.59861.19650.20190.3443-0.2716-0.04710.4148-0.01110.167271.17515.952-22.613
622.3367-1.02091.82530.7706-2.24377.96110.0687-0.1064-0.044-0.10320.0060.01330.30710.1796-0.07460.2281-0.0301-0.06850.251-0.01620.173462.9872.636-31.242
634.8149-3.33684.80943.0998-4.01877.01550.0060.08230.24280.2822-0.1281-0.1006-0.34860.41930.1220.1912-0.0085-0.02880.2003-0.00310.177154.6326.259-49.929
641.2851-0.052-3.98990.00410.170613.5523-0.1494-0.0002-0.0979-0.01340.00040.0140.1297-0.83710.1490.26240.1646-0.0160.68890.04760.273939.12212.663-41.2
6518.57261.176115.24360.07630.966812.5127-0.02870.30340.01890.01750.00580.013-0.00530.24280.0230.28580.07260.09420.8164-0.03480.210539.35414.69-27.762
661.8281-0.35450.02644.19035.84938.3186-0.0114-0.4721-0.1071-0.10330.132-0.0731-0.13950.0429-0.12060.37490.0079-0.00120.4169-0.04520.112148.328.979-36.915
672.38872.1449-0.15712.0322-0.24320.35450.0813-0.1011-0.24630.0317-0.0096-0.1186-0.00970.0236-0.07170.18620.0057-0.03060.2593-0.01580.225238.941-12.566-54.95
681.6945-3.9833-3.053914.212211.81829.9502-0.1563-0.1023-0.2688-0.90220.6525-0.3656-0.92750.6192-0.49610.3937-0.15810.21480.4739-0.10070.407516.883-5.039-39.789
690.1485-0.64532.9522.8663-13.249861.5660.104-0.0381-0.0125-0.22470.09680.04460.4657-0.2111-0.20081.2232-0.39740.10250.89640.04180.079516.029-6.492-25.243
702.69812.73171.91372.78191.95421.38290.4672-0.44530.04050.4066-0.49940.0030.2852-0.40790.03230.44510.0390.33020.4644-0.05790.3966.839-9.013-33.387
710.5745-0.2046-0.5960.07670.21230.63160.72910.04190.5956-0.2654-0.0295-0.2011-0.7361-0.0226-0.69961.09420.11070.44310.0851-0.12971.37069.0540.314-35.485
720.1038-0.054-0.01914.39888.025814.70750.27380.02080.0644-0.0419-0.1607-0.10140.1419-0.3065-0.1130.7508-0.04440.19340.3505-0.0610.496117.4483.184-38.057
733.13913.4585-0.92974.99922.256110.34320.8377-0.28240.56880.45530.29820.3301-1.37811.5901-1.13590.4621-0.3080.14630.3573-0.20670.38825.01-6.662-44.671
7421.75964.715-2.40469.81942.87661.6237-0.2237-0.58770.00210.37490.4807-0.33080.13710.3583-0.2570.25820.01240.10470.3437-0.13660.393321.494-15.255-42.072
755.80653.8744.249913.9973-2.86896.01881.4560.0128-0.68512.3354-0.27140.88530.38750.05-1.18460.5397-0.0128-0.01270.4113-0.1210.291417.739-13.044-35.397
763.30133.86141.134214.43837.60794.40050.1998-0.43830.13580.5032-0.28860.41870.1770.04140.08880.1966-0.04120.24580.4787-0.05650.5117.057-9.049-38.288
775.08280.850.87793.32590.35740.16660.030.12970.010.026-0.03960.25220.00840.0280.00950.20330.0013-0.02860.29050.0460.189630.351-12.762-57.586
7816.31914.1002-2.31691.83540.47494.16610.1619-0.2104-0.06370.0716-0.17780.0220.33890.16170.01590.23810.0743-0.05980.2153-0.0160.147752.731-7.68-46.745
798.5474-6.02671.4768.17815.04329.7035-0.04170.39880.58980.8630.4874-0.76981.28771.3382-0.44580.18710.1068-0.08470.80860.01470.079670.9580.143-39.141
8037.1875-18.35129.357626.06646.02459.01450.32770.7067-0.56871.15060.1142-0.20340.92880.4783-0.4420.61130.09160.11950.27760.02780.216764.341-6.405-37.804
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 11
2X-RAY DIFFRACTION2A12 - 35
3X-RAY DIFFRACTION3A36 - 50
4X-RAY DIFFRACTION4A51 - 62
5X-RAY DIFFRACTION5A63 - 73
6X-RAY DIFFRACTION6A74 - 93
7X-RAY DIFFRACTION7A94 - 113
8X-RAY DIFFRACTION8A114 - 132
9X-RAY DIFFRACTION9A133 - 139
10X-RAY DIFFRACTION10A140 - 148
11X-RAY DIFFRACTION11A149 - 154
12X-RAY DIFFRACTION12A155 - 169
13X-RAY DIFFRACTION13A170 - 202
14X-RAY DIFFRACTION14A203 - 211
15X-RAY DIFFRACTION15A212 - 216
16X-RAY DIFFRACTION16A217 - 229
17X-RAY DIFFRACTION17A230 - 240
18X-RAY DIFFRACTION18A241 - 251
19X-RAY DIFFRACTION19A252 - 264
20X-RAY DIFFRACTION20A265 - 274
21X-RAY DIFFRACTION21B3 - 12
22X-RAY DIFFRACTION22B13 - 36
23X-RAY DIFFRACTION23B37 - 49
24X-RAY DIFFRACTION24B50 - 54
25X-RAY DIFFRACTION25B55 - 66
26X-RAY DIFFRACTION26B67 - 77
27X-RAY DIFFRACTION27B78 - 91
28X-RAY DIFFRACTION28B92 - 106
29X-RAY DIFFRACTION29B107 - 117
30X-RAY DIFFRACTION30B118 - 137
31X-RAY DIFFRACTION31B138 - 158
32X-RAY DIFFRACTION32B159 - 168
33X-RAY DIFFRACTION33B169 - 198
34X-RAY DIFFRACTION34B199 - 219
35X-RAY DIFFRACTION35B220 - 227
36X-RAY DIFFRACTION36B228 - 235
37X-RAY DIFFRACTION37B236 - 244
38X-RAY DIFFRACTION38B245 - 253
39X-RAY DIFFRACTION39B254 - 265
40X-RAY DIFFRACTION40B266 - 274
41X-RAY DIFFRACTION41C3 - 35
42X-RAY DIFFRACTION42C36 - 49
43X-RAY DIFFRACTION43C50 - 61
44X-RAY DIFFRACTION44C62 - 67
45X-RAY DIFFRACTION45C68 - 87
46X-RAY DIFFRACTION46C88 - 105
47X-RAY DIFFRACTION47C106 - 115
48X-RAY DIFFRACTION48C116 - 128
49X-RAY DIFFRACTION49C129 - 139
50X-RAY DIFFRACTION50C140 - 145
51X-RAY DIFFRACTION51C146 - 159
52X-RAY DIFFRACTION52C160 - 170
53X-RAY DIFFRACTION53C171 - 179
54X-RAY DIFFRACTION54C180 - 185
55X-RAY DIFFRACTION55C186 - 206
56X-RAY DIFFRACTION56C207 - 222
57X-RAY DIFFRACTION57C223 - 237
58X-RAY DIFFRACTION58C238 - 257
59X-RAY DIFFRACTION59C258 - 265
60X-RAY DIFFRACTION60C266 - 274
61X-RAY DIFFRACTION61D2 - 20
62X-RAY DIFFRACTION62D21 - 36
63X-RAY DIFFRACTION63D37 - 50
64X-RAY DIFFRACTION64D51 - 64
65X-RAY DIFFRACTION65D65 - 71
66X-RAY DIFFRACTION66D72 - 93
67X-RAY DIFFRACTION67D94 - 121
68X-RAY DIFFRACTION68D122 - 127
69X-RAY DIFFRACTION69D128 - 134
70X-RAY DIFFRACTION70D135 - 149
71X-RAY DIFFRACTION71D150 - 155
72X-RAY DIFFRACTION72D156 - 165
73X-RAY DIFFRACTION73D166 - 179
74X-RAY DIFFRACTION74D180 - 189
75X-RAY DIFFRACTION75D190 - 207
76X-RAY DIFFRACTION76D208 - 216
77X-RAY DIFFRACTION77D217 - 237
78X-RAY DIFFRACTION78D238 - 257
79X-RAY DIFFRACTION79D258 - 266
80X-RAY DIFFRACTION80D267 - 274

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万見について

-
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://pdbjlvh1.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