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Structure paper

タイトルExperimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
ジャーナル・号・ページBiochemistry, Vol. 54, Page 909-931, Year 2015
掲載日2013年7月11日 (構造データの登録日)
著者Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. ...Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
リンクBiochemistry / PubMed:25540822
手法X線回折
解像度1.05 - 2.7 Å
構造データ

PDB-4ln5:
Crystal structure of a trap periplasmic solute binding protein from burkholderia ambifaria (Bamb_6123), TARGET EFI-510059, with bound glycerol and chloride ion
手法: X-RAY DIFFRACTION / 解像度: 2.1 Å

PDB-4mco:
Crystal structure of a TRAP periplasmic solute binding protein from Rhodoferax ferrireducens (Rfer_1840), target EFI-510211, with bound malonate
手法: X-RAY DIFFRACTION / 解像度: 1.6 Å

PDB-4mev:
Crystal structure of a TRAP periplasmic solute binding protein from Rhodoferax ferrireducens (Rfer_1840), Target EFI-510211, with bound malonate, space group I422
手法: X-RAY DIFFRACTION / 解像度: 1.8 Å

PDB-4mhf:
Crystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_3107), target EFI-510173, with bound alpha/beta D-Glucuronate, space group P21
手法: X-RAY DIFFRACTION / 解像度: 1.46 Å

PDB-4mij:
Crystal structure of a Trap periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_3107), target EFI-510173, with bound alpha/beta D-Galacturonate, space group P21
手法: X-RAY DIFFRACTION / 解像度: 1.1 Å

PDB-4mnc:
Crystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_4736), Target EFI-510156, with bound benzoyl formate, space group P21
手法: X-RAY DIFFRACTION / 解像度: 1.05 Å

PDB-4mni:
Crystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_4736), Target EFI-510156, with bound benzoyl formate, space group P6522
手法: X-RAY DIFFRACTION / 解像度: 1.9 Å

PDB-4mx6:
Crystal structure of a trap periplasmic solute binding protein from shewanella oneidensis (SO_3134), target EFI-510275, with bound succinate
手法: X-RAY DIFFRACTION / 解像度: 1.1 Å

PDB-4n15:
Crystal structure of a TRAP periplasmic solute binding protein from Burkholderia ambifaria (BAM_6123), Target EFI-510059, with bound beta-D-glucuronate
手法: X-RAY DIFFRACTION / 解像度: 1.651 Å

PDB-4n17:
Crystal structure of a TRAP periplasmic solute binding protein from Burkholderia ambifaria (BAM_6123), Target EFI-510059, With bound beta-D-galacturonate
手法: X-RAY DIFFRACTION / 解像度: 1.501 Å

PDB-4n4u:
Crystal structure of ABC transporter solute binding protein BB0719 from Bordetella bronchiseptica RB50, TARGET EFI-510049
手法: X-RAY DIFFRACTION / 解像度: 1.57 Å

PDB-4n6d:
Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens DSM2638 (Desal_3247), Target EFI-510112, phased with I3C, open complex, C-terminus of symmetry mate bound in ligand binding site
手法: X-RAY DIFFRACTION / 解像度: 1.701 Å

PDB-4n6k:
Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens DSM2638, Target EFI-510113 (Desal_0342), complex with diglycerolphosphate
手法: X-RAY DIFFRACTION / 解像度: 1.2 Å

PDB-4n8g:
Crystal structure of a TRAP periplasmic solute binding protein from Chromohalobacter salexigens DSM 3043 (Csal_0660), Target EFI-501075, with bound D-alanine-D-alanine
手法: X-RAY DIFFRACTION / 解像度: 1.502 Å

PDB-4n8y:
Crystal structure of a trap periplasmic solute binding protein from bradyrhizobium sp. btai1 b (bbta_0128), target EFI-510056 (bbta_0128), complex with alpha/beta-d-galacturonate
手法: X-RAY DIFFRACTION / 解像度: 1.5 Å

PDB-4n91:
Crystal structure of a trap periplasmic solute binding protein from anaerococcus prevotii dsm 20548 (Apre_1383), target EFI-510023, with bound alpha/beta d-glucuronate
手法: X-RAY DIFFRACTION / 解像度: 1.7 Å

PDB-4nap:
Crystal structure of a trap periplasmic solute binding protein from Desulfovibrio alaskensis G20 (DDE_0634), target EFI-510102, with bound d-tryptophan
手法: X-RAY DIFFRACTION / 解像度: 2.3 Å

PDB-4nf0:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM PSEUDOMONAS AERUGINOSA PAO1 (PA4616), TARGET EFI-510182, WITH BOUND L-Malate
手法: X-RAY DIFFRACTION / 解像度: 1.85 Å

PDB-4ng7:
Crystal structure of a TRAP periplasmic solute binding protein from Citrobacter koseri (CKO_04899), Target EFI-510094, apo, open structure
手法: X-RAY DIFFRACTION / 解像度: 2.3 Å

PDB-4ngu:
Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio alaskensis G20 (Dde_1548), Target EFI-510103, with bound D-Ala-D-Ala
手法: X-RAY DIFFRACTION / 解像度: 2.5 Å

PDB-4nhb:
Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio desulfuricans (Ddes_1525), Target EFI-510107, with bound sn-glycerol-3-phosphate
手法: X-RAY DIFFRACTION / 解像度: 1.902 Å

PDB-4nn3:
Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens (Desal_2161), Target EFI-510109, with bound orotic acid
手法: X-RAY DIFFRACTION / 解像度: 1.4 Å

PDB-4nq8:
Crystal structure of a trap periplasmic solute binding protein from Bordetella bronchispeptica (bb3421), target EFI-510039, with density modeled as pantoate
手法: X-RAY DIFFRACTION / 解像度: 1.5 Å

PDB-4nx1:
Crystal structure of a trap periplasmic solute binding protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate
手法: X-RAY DIFFRACTION / 解像度: 1.6 Å

PDB-4o7m:
Crystal structure of a trap periplasmic solute binding protein from shewanella loihica PV-4, target EFI-510273, with bound L-malate
手法: X-RAY DIFFRACTION / 解像度: 1.5 Å

PDB-4o8m:
Crystal structure of a trap periplasmic solute binding protein actinobacillus succinogenes 130z, target EFI-510004, with bound L-galactonate
手法: X-RAY DIFFRACTION / 解像度: 1.7 Å

PDB-4o94:
Crystal structure of a trap periplasmic solute binding protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate
手法: X-RAY DIFFRACTION / 解像度: 2 Å

PDB-4oa4:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SHEWANELLA LOIHICA PV-4 (Shew_1446), TARGET EFI-510273, WITH BOUND SUCCINATE
手法: X-RAY DIFFRACTION / 解像度: 1.6 Å

PDB-4oan:
Crystal structure of a TRAP periplasmic solute binding protein from rhodopseudomonas palustris HaA2 (RPB_2686), TARGET EFI-510221, with density modeled as (S)-2-hydroxy-2-methyl-3-oxobutanoate ((S)-2-Acetolactate)
手法: X-RAY DIFFRACTION / 解像度: 1.35 Å

PDB-4ovp:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER sp. NAS-14.1, TARGET EFI-510292, WITH BOUND ALPHA-D-MANURONATE
手法: X-RAY DIFFRACTION / 解像度: 1.7 Å

PDB-4ovq:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS, TARGET EFI-510230, WITH BOUND BETA-D-GLUCURONATE
手法: X-RAY DIFFRACTION / 解像度: 1.501 Å

PDB-4ovr:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM XANTHOBACTER AUTOTROPHICUS PY2, TARGET EFI-510329, WITH BOUND BETA-D-GALACTURONATE
手法: X-RAY DIFFRACTION / 解像度: 1.65 Å

PDB-4ovs:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFUROSPIRILLUM DELEYIANUM DSM 6946 (Sdel_0447), TARGET EFI-510309, WITH BOUND SUCCINATE
手法: X-RAY DIFFRACTION / 解像度: 1.8 Å

PDB-4ovt:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM OCHROBACTERIUM ANTHROPI (Oant_3902), TARGET EFI-510153, WITH BOUND L-FUCONATE
手法: X-RAY DIFFRACTION / 解像度: 1.8 Å

PDB-4p1e:
Crystal structure of a trap periplasmic solute binding protein from escherichia fergusonii (efer_1530), target EFI-510119, apo open structure, phased with iodide
手法: X-RAY DIFFRACTION / 解像度: 1.9 Å

PDB-4p1l:
Crystal structure of a trap periplasmic solute binding protein from chromohalobacter salexigens dsm 3043 (csal_2479), target EFI-510085, with bound d-glucuronate, spg i213
手法: X-RAY DIFFRACTION / 解像度: 1.7 Å

PDB-4p3l:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM CHROMOHALOBACTER SALEXIGENS DSM 3043 (Csal_2479), TARGET EFI-510085, WITH BOUND GLUCURONATE, SPG P6122
手法: X-RAY DIFFRACTION / 解像度: 1.8 Å

PDB-4p47:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM OCHROBACTRUM ANTHROPI (Oant_4429), TARGET EFI-510151, C-TERMIUS BOUND IN LIGAND BINDING POCKET
手法: X-RAY DIFFRACTION / 解像度: 1.3 Å

PDB-4p56:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM BORDETELLA BRONCHISEPTICA, TARGET EFI-510038 (BB2442), WITH BOUND (R)-MANDELATE and (S)-MANDELATE
手法: X-RAY DIFFRACTION / 解像度: 1.9 Å

PDB-4p8b:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RALSTONIA EUTROPHA H16 (H16_A1328), TARGET EFI-510189, WITH BOUND (S)-2-hydroxy-2-methyl-3-oxobutanoate ((S)-2-Acetolactate)
手法: X-RAY DIFFRACTION / 解像度: 1.3 Å

PDB-4p9k:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM VERMINEPHROBACTER EISENIAE EF01-2 (Veis_3954, TARGET EFI-510324) A NEPHRIDIAL SYMBIONT OF THE EARTHWORM EISENIA FOETIDA, BOUND TO D-ERYTHRONATE WITH RESIDUAL DENSITY SUGGESTIVE OF SUPERPOSITION WITH COPURIFIED ALTERNATIVE LIGAND.
手法: X-RAY DIFFRACTION / 解像度: 1.4 Å

PDB-4paf:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RUEGERIA POMEROYI DSS-3 (SPO1773, TARGET EFI-510260) WITH BOUND 3,4-DIHYDROXYBENZOATE
手法: X-RAY DIFFRACTION / 解像度: 1.6 Å

PDB-4pai:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RUEGERIA POMEROYI DSS-3 (SPO1773, TARGET EFI-510260) WITH BOUND 3-HYDROXYBENZOATE
手法: X-RAY DIFFRACTION / 解像度: 1.4 Å

PDB-4pak:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM VERMINEPHROBACTER EISENIAE EF01-2 (Veis_3954, TARGET EFI-510324) A NEPHRIDIAL SYMBIONT OF THE EARTHWORM EISENIA FOETIDA, BOUND TO (R)-PANTOIC ACID
手法: X-RAY DIFFRACTION / 解像度: 1.2 Å

PDB-4pbh:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RUEGERIA POMEROYI DSS-3 (SPO1773, TARGET EFI-510260) WITH BOUND BENZOIC ACID
手法: X-RAY DIFFRACTION / 解像度: 1.2 Å

PDB-4pbq:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM HAEMOPHILUS INFLUENZAE RdAW (HICG_00826, TARGET EFI-510123) WITH BOUND L-GULONATE
手法: X-RAY DIFFRACTION / 解像度: 1.65 Å

PDB-4pc9:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSENBACTER DENITRIFICANS OCh 114 (RD1_1052, TARGET EFI-510238) WITH BOUND D-MANNONATE
手法: X-RAY DIFFRACTION / 解像度: 1.3 Å

PDB-4pcd:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS OCh 114 (RD1_1052, TARGET EFI-510238) WITH BOUND L-GALACTONATE
手法: X-RAY DIFFRACTION / 解像度: 1.7 Å

PDB-4pdd:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM POLAROMONAS SP JS666 (Bpro_0088, TARGET EFI-510167) BOUND TO D-ERYTHRONATE
手法: X-RAY DIFFRACTION / 解像度: 1.7 Å

PDB-4pdh:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM POLAROMONAS SP JS666 (Bpro_1871, TARGET EFI-510164) BOUND TO D-ERYTHRONATE
手法: X-RAY DIFFRACTION / 解像度: 1.8 Å

PDB-4pe3:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RHODOBACTER SPHAEROIDES (Rsph17029_3620, TARGET EFI-510199), APO OPEN STRUCTURE
手法: X-RAY DIFFRACTION / 解像度: 1.35 Å

PDB-4pet:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM COLWELLIA PSYCHRERYTHRAEA (CPS_0129, TARGET EFI-510097) WITH BOUND CALCIUM AND PYRUVATE
手法: X-RAY DIFFRACTION / 解像度: 1.9 Å

PDB-4pf6:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS (RD1_0742, TARGET EFI-510239) WITH BOUND 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID (KDO)
手法: X-RAY DIFFRACTION / 解像度: 1.75 Å

PDB-4pf8:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER sp. NAS-14.1 (TARGET EFI-510299) WITH BOUND BETA-D-GALACTURONATE
手法: X-RAY DIFFRACTION / 解像度: 1.5 Å

PDB-4pfb:
Crystal structure of a TRAP periplasmic solute binding protein from Fusobacterium nucleatun (FN1258, TARGET EFI-510120) with bound SN-glycerol-3-phosphate
手法: X-RAY DIFFRACTION / 解像度: 2.7 Å

PDB-4pfi:
Crystal structure of a tRAP periplasmic solute binding protein from marinobacter aquaeolei VT8 (Maqu_2829, TARGET EFI-510133), apo open structure
手法: X-RAY DIFFRACTION / 解像度: 2.3024 Å

PDB-4pfr:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RHODOBACTER SPHAEROIDES (Rsph17029_3541, TARGET EFI-510203), APO OPEN PARTIALLY DISORDERED
手法: X-RAY DIFFRACTION / 解像度: 2.6 Å

PDB-4pgn:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO ALASKENSIS G20 (Dde_0634, TARGET EFI-510120) WITH BOUND INDOLE PYRUVATE
手法: X-RAY DIFFRACTION / 解像度: 1.8 Å

PDB-4pgp:
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO ALASKENSIS G20 (Dde_0634, TARGET EFI-510120) WITH BOUND 3-INDOLE ACETIC ACID
手法: X-RAY DIFFRACTION / 解像度: 2.25 Å

PDB-4uab:
Crystal structure of a TRAP periplasmic solute binding protein from Chromohalobacter salexigens DSM 3043 (Csal_0678), Target EFI-501078, with bound ethanolamine
手法: X-RAY DIFFRACTION / 解像度: 1.4 Å

化合物

ChemComp-CL:
Unknown entry / クロリド

ChemComp-GOL:
GLYCEROL / グリセロ-ル

ChemComp-HOH:
WATER

ChemComp-MLI:
MALONATE ION / マロナ-ト

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / pH緩衝剤*YM

ChemComp-CIT:
CITRIC ACID / クエン酸

ChemComp-BDP:
beta-D-glucopyranuronic acid / β-D-グルコピラヌロン酸

ChemComp-GCU:
alpha-D-glucopyranuronic acid / α-D-グルコピラヌロン酸

ChemComp-EDO:
1,2-ETHANEDIOL / エチレングリコ-ル

ChemComp-GTR:
beta-D-galactopyranuronic acid / β-D-ガラクトピラヌロン酸

ChemComp-ADA:
alpha-D-galactopyranuronic acid / α-D-ガラクトピラヌロン酸

ChemComp-173:
BENZOYL-FORMIC ACID / フェニルグリオキシル酸

ChemComp-SO4:
SULFATE ION / 硫酸ジアニオン

ChemComp-SIN:
SUCCINIC ACID / コハク酸

ChemComp-MG:
Unknown entry / マグネシウムジカチオン

ChemComp-CA:
Unknown entry / カルシウムジカチオン

ChemComp-I3C:
5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-アミノ-2,4,6-トリヨ-ドイソフタル酸

ChemComp-X3X:
bis[(2S)-2,3-dihydroxypropyl] hydrogen phosphate

ChemComp-DAL:
D-ALANINE / D-アラニン

ChemComp-PG4:
TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル / 沈殿剤*YM

ChemComp-DTR:
D-TRYPTOPHAN / D-トリプトファン

ChemComp-LMR:
(2S)-2-hydroxybutanedioic acid / L-りんご酸

ChemComp-IOD:
IODIDE ION / ヨ-ジド

ChemComp-G3P:
SN-GLYCEROL-3-PHOSPHATE / L-グリセロ-ル3-りん酸

ChemComp-PGE:
TRIETHYLENE GLYCOL / トリエチレングリコ-ル

ChemComp-ORO:
OROTIC ACID / オロチン酸

ChemComp-PAF:
PANTOATE

ChemComp-X1X:
alpha-D-talopyranuronic acid

ChemComp-2Q2:
L-galactonic acid / L-ガラクトン酸

ChemComp-X2X:
(2S)-2-hydroxy-2-methyl-3-oxobutanoic acid / (S)-2-アセト乳酸

ChemComp-MAV:
alpha-D-mannopyranuronic acid

ChemComp-LFC:
6-deoxy-L-galactonic acid / L-フコン酸

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル

ChemComp-RMN:
(R)-MANDELIC ACID / (R)-(-)-マンデル酸

ChemComp-SMN:
(S)-MANDELIC ACID / (S)-マンデル酸

ChemComp-EAX:
(2R,3R)-2,3,4-trihydroxybutanoic acid / D-エリトロン酸

ChemComp-DHB:
3,4-DIHYDROXYBENZOIC ACID / プロトカテク酸

ChemComp-3HB:
3-HYDROXYBENZOIC ACID / 3-ヒドロキシ安息香酸

ChemComp-BEZ:
BENZOIC ACID / 安息香酸

ChemComp-2UF:
L-gulonate / L-グロン酸

ChemComp-MES:
2-(N-MORPHOLINO)-ETHANESULFONIC ACID / 2-モルホリノエタンスルホン酸 / pH緩衝剤*YM

ChemComp-CS2:
D-MANNONIC ACID / D-マンノン酸

ChemComp-MLA:
MALONIC ACID / マロン酸

ChemComp-FMT:
FORMIC ACID / ギ酸

ChemComp-IMD:
IMIDAZOLE / 1H-イミダゾ-ル-3-カチオン

ChemComp-ACT:
ACETATE ION / 酢酸イオン

ChemComp-ZN:
Unknown entry

ChemComp-PYR:
PYRUVIC ACID / ピルビン酸

ChemComp-KDO:
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / (2R)-2-デオキソ-2-ヒドロキシ-2,6-オキシ-3,6-ジデオキシ-D-manno-2-オクツロソン酸

ChemComp-NA:
Unknown entry / ナトリウムカチオン

ChemComp-MLT:
D-MALATE / D-りんご酸

ChemComp-3IO:
3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID / インド-ル-3-ピルビン酸

ChemComp-IAC:
1H-INDOL-3-YLACETIC ACID / インド-ル酢酸 / ホルモン*YM

ChemComp-ETA:
ETHANOLAMINE / エタノ-ルアミン

由来
  • burkholderia ambifaria (バクテリア)
  • rhodoferax ferrireducens (バクテリア)
  • polaromonas (バクテリア)
  • polaromonas sp. (バクテリア)
  • shewanella oneidensis (バクテリア)
  • bordetella bronchiseptica (気管支敗血症菌)
  • desulfovibrio salexigens (バクテリア)
  • chromohalobacter salexigens (バクテリア)
  • bradyrhizobium sp. (根粒菌)
  • anaerococcus prevoti (バクテリア)
  • desulfovibrio alaskensis (バクテリア)
  • pseudomonas aeruginosa (緑膿菌)
  • citrobacter koseri (バクテリア)
  • desulfovibrio desulfuricans subsp. desulfuricans (バクテリア)
  • sulfitobacter sp. nas-14.1 (バクテリア)
  • shewanella loihica (バクテリア)
  • actinobacillus succinogenes (バクテリア)
  • rhodopseudomonas palustris (光合成細菌)
  • sulfitobacter sp. (バクテリア)
  • roseobacter denitrificans (バクテリア)
  • xanthobacter autotrophicus (バクテリア)
  • sulfurospirillum deleyianum (バクテリア)
  • ochrobactrum anthropi (バクテリア)
  • escherichia fergusonii (バクテリア)
  • cupriavidus necator (バクテリア)
  • verminephrobacter eiseniae (バクテリア)
  • ruegeria pomeroyi (バクテリア)
  • haemophilus influenzae (インフルエンザ菌)
  • polaromonas sp. js666 (バクテリア)
  • rhodobacter sphaeroides (バクテリア)
  • colwellia psychrerythraea (バクテリア)
  • fusobacterium nucleatum subsp. nucleatum (バクテリア)
  • marinobacter aquaeolei (バクテリア)
  • desulfovibrio desulfuricans (バクテリア)
キーワードTRANSPORT PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics / TRAP periplasmic solute binding family / ABC PERIPLASMIC SOLUTE BINDING FAMILY / PROTEIN TRANSPORT / PROTEIN BINDING / MEMBRANE PROTEIN/PROTEIN TRANSPORT / MEMBRANE PROTEIN-PROTEIN TRANSPORT complex / SOLUTE-BINDING PROTEIN

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万見文献について

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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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万見文献

EMDB/PDB/SASBDBから引用されている文献のデータベース

  • EMDB/PDB/SASBDBのエントリから引用されている文献のデータベースです
  • Pubmedのデータを利用しています

関連情報:EMDB / PDB / SASBDB / 万見 (Yorodumi) / EMN文献 / 新しいEM Navigatorと万見の変更点

他の情報も見る