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Structure paper

TitleStructural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Journal, issue, pagesMicrobiol Resour Announc, Vol. 14, Page e0020025-e0020025, Year 2025
Publish dateOct 25, 2016 (structure data deposition date)
AuthorsInniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. ...Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
External linksMicrobiol Resour Announc / PubMed:40391899
MethodsX-ray diffraction
Resolution1.05 - 2.75 Å
Structure data

PDB-5tr3:
2.5 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Pseudomonas putida in Complex with FAD.
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-5tv2:
Crystal structure of a fragment (1-405) of an elongation factor G from Vibrio vulnificus CMCP6
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-5ty0:
2.22 Angstrom Crystal Structure of N-terminal Fragment (residues 1-419) of Elongation Factor G from Legionella pneumophila.
Method: X-RAY DIFFRACTION / Resolution: 2.22 Å

PDB-5u1o:
2.3 Angstrom Resolution Crystal Structure of Glutathione Reductase from Vibrio parahaemolyticus in Complex with FAD.
Method: X-RAY DIFFRACTION / Resolution: 2.31 Å

PDB-5u2g:
2.6 Angstrom Resolution Crystal Structure of Penicillin-Binding Protein 1A from Haemophilus influenzae
Method: X-RAY DIFFRACTION / Resolution: 2.61 Å

PDB-5u47:
1.95 Angstrom Resolution Crystal Structure of Penicillin Binding Protein 2X from Streptococcus thermophilus
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-5ue1:
Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase in complex with adenine from Vibrio fischeri ES114
Method: X-RAY DIFFRACTION / Resolution: 1.14 Å

PDB-5ume:
Crystal Structure of 5,10-Methylenetetrahydrofolate Reductase MetF from Haemophilus influenzae
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5us8:
2.15 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-5usw:
The crystal structure of 7,8-dihydropteroate synthase from Vibrio fischeri ES114
Method: X-RAY DIFFRACTION / Resolution: 1.643 Å

PDB-5usx:
Crystal structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 in complex with NADP and FAD
Method: X-RAY DIFFRACTION / Resolution: 2.603 Å

PDB-5utx:
Crystal structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 - apo form
Method: X-RAY DIFFRACTION / Resolution: 2.46 Å

PDB-5uu6:
The crystal structure of nitroreductase A from Vibrio parahaemolyticus RIMD 2210633
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-5uwy:
The crystal structure of thioredoxin reductase from Streptococcus pyogenes MGAS5005
Method: X-RAY DIFFRACTION / Resolution: 2.72 Å

PDB-5ux9:
The crystal structure of chloramphenicol acetyltransferase from Vibrio fischeri ES114
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5v36:
1.88 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus mutans UA159 in Complex with FAD
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-5vdn:
1.55 Angstrom Resolution Crystal Structure of Glutathione Reductase from Yersinia pestis in Complex with FAD
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-5vfb:
1.36 Angstrom Resolution Crystal Structure of Malate Synthase G from Pseudomonas aeruginosa in Complex with Glycolic Acid.
Method: X-RAY DIFFRACTION / Resolution: 1.36 Å

PDB-5vh6:
2.6 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-406) of Elongation Factor G from Bacillus subtilis.
Method: X-RAY DIFFRACTION / Resolution: 2.61 Å

PDB-5wi5:
2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium.
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-5wp0:
Crystal structure of NAD synthetase NadE from Vibrio fischeri
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-6aon:
1.72 Angstrom Resolution Crystal Structure of 2-Oxoglutarate Dehydrogenase Complex Subunit Dihydrolipoamide Dehydrogenase from Bordetella pertussis in Complex with FAD
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-6aoo:
2.15 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-6awa:
1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Pseudomonas putida in Complex with FAD and Adenosine-5'-monophosphate.
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-6azi:
1.75 Angstrom Resolution Crystal Structure of D-alanyl-D-alanine Endopeptidase from Enterobacter cloacae in Complex with Covalently Bound Boronic Acid
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-6b4o:
1.73 Angstrom Resolution Crystal Structure of Glutathione Reductase from Enterococcus faecalis in Complex with FAD
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-6b5f:
Crystal structure of nicotinate mononucleotide-5,6-dimethylbenzimidazole phosphoribosyltransferase CobT from Yersinia enterocolitica
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-6b8d:
1.78 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-405) of Elongation Factor G from Haemophilus influenzae
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-6bal:
2.1 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae in Complex with L-Malate
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-6bk7:
1.83 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-404) of Elongation Factor G from Enterococcus faecalis
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-6blb:
1.88 Angstrom Resolution Crystal Structure Holliday Junction ATP-dependent DNA Helicase (RuvB) from Pseudomonas aeruginosa in Complex with ADP
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-6bq9:
2.55 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-493) of DNA Topoisomerase IV Subunit A from Pseudomonas putida
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-6bz0:
1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Acinetobacter baumannii in Complex with FAD.
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-6c8q:
Crystal structure of NAD synthetase (NadE) from Enterococcus faecalis in complex with NAD+
Method: X-RAY DIFFRACTION / Resolution: 2.583 Å

PDB-6cmz:
2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide Dehydrogenase from Burkholderia cenocepacia in Complex with FAD and NAD
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-6cn1:
2.75 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Pseudomonas putida in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium
Method: X-RAY DIFFRACTION / Resolution: 2.75 Å

PDB-6czp:
2.2 Angstrom Resolution Crystal Structure Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB from Vibrio vulnificus in Complex with FMN
Method: X-RAY DIFFRACTION / Resolution: 2.24 Å

PDB-6e5y:
1.50 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis in Complex with AMP.
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6muq:
1.67 Angstrom Resolution Crystal Structure of Murein-DD-endopeptidase from Yersinia enterocolitica.
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-6n0i:
2.60 Angstrom Resolution Crystal Structure of Elongation Factor G 2 from Pseudomonas putida.
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-6n7f:
1.90 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus pyogenes in Complex with FAD.
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-6nfp:
1.7 Angstrom Resolution Crystal Structure of Arginase from Bacillus subtilis subsp. subtilis str. 168
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-6nkj:
1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with (2R)-2-(phosphonooxy)propanoic acid.
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-6po4:
2.1 Angstrom Resolution Crystal Structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (mtnN) from Haemophilus influenzae PittII.
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-6pu9:
Crystal Structure of the Type B Chloramphenicol O-Acetyltransferase from Vibrio vulnificus
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-6pua:
The 2.0 A Crystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-6pxa:
The crystal structure of chloramphenicol acetyltransferase-like protein from Vibrio fischeri ES114 in complex with taurocholic acid
Method: X-RAY DIFFRACTION / Resolution: 1.82 Å

PDB-6w2z:
Crystal Structure of the Beta Lactamase Class A PenP from Bacillus subtilis in the Complex with the Non-beta- lactam Beta-lactamase Inhibitor Avibactam
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-9bzn:
High resolution structure of class A Beta-lactamase from Bordetella bronchiseptica RB50
Method: X-RAY DIFFRACTION / Resolution: 1.05 Å

PDB-9bzq:
Structure of Class A Beta-lactamase from Bordetella bronchiseptica RB50 in a complex with Avibactam
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-9bzr:
Structure of Class A Beta-lactamase from Bordetella bronchiseptica RB50 in a complex with clavulonate
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

Chemicals

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

ChemComp-GOL:
GLYCEROL

ChemComp-HOH:
WATER

ChemComp-NA:
Unknown entry

ChemComp-BGC:
beta-D-glucopyranose

ChemComp-SO4:
SULFATE ION

ChemComp-CL:
Unknown entry

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-ACT:
ACETATE ION

ChemComp-9DA:
9-DEAZAADENINE

ChemComp-CA:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-ACY:
ACETIC ACID

ChemComp-FMT:
FORMIC ACID

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

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-ADN:
ADENOSINE

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-PO4:
PHOSPHATE ION

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

ChemComp-MES:
2-(N-MORPHOLINO)-ETHANESULFONIC ACID / pH buffer*YM

ChemComp-MG:
Unknown entry

ChemComp-BME:
BETA-MERCAPTOETHANOL

ChemComp-BDF:
beta-D-fructopyranose

ChemComp-K:
Unknown entry

ChemComp-NI:
NICKEL (II) ION

ChemComp-GOA:
GLYCOLIC ACID

ChemComp-0V5:
(2R)-2-(phosphonooxy)propanoic acid

ChemComp-EPU:
URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

ChemComp-BO4:
BORATE ION

ChemComp-LMR:
(2S)-2-hydroxybutanedioic acid

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

ChemComp-MLT:
D-MALATE

ChemComp-MLA:
MALONIC ACID

ChemComp-RBF:
RIBOFLAVIN

ChemComp-BTB:
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

ChemComp-URE:
UREA

ChemComp-CIT:
CITRIC ACID

ChemComp-HCS:
2-AMINO-4-MERCAPTO-BUTYRIC ACID

ChemComp-ADE:
ADENINE

ChemComp-BO3:
BORIC ACID

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM

ChemComp-TCH:
TAUROCHOLIC ACID

ChemComp-NXL:
(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / antibiotic, inhibitor*YM

ChemComp-SIN:
SUCCINIC ACID

ChemComp-TEM:
N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE

Source
  • pseudomonas putida (strain atcc 47054 / dsm 6125 / ncimb 11950 / kt2440) (bacteria)
  • vibrio vulnificus (bacteria)
  • legionella pneumophila subsp. pneumophila (strain philadelphia 1 / atcc 33152 / dsm 7513) (bacteria)
  • vibrio parahaemolyticus serotype o3:k6 (strain rimd 2210633) (bacteria)
  • haemophilus influenzae (bacteria)
  • streptococcus thermophilus (strain atcc baa-250 / lmg 18311) (bacteria)
  • vibrio fischeri (strain atcc 700601 / es114) (bacteria)
  • haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd) (bacteria)
  • bordetella pertussis (strain tohama i / atcc baa-589 / nctc 13251) (bacteria)
  • vibrio vulnificus cmcp6 (bacteria)
  • streptococcus pyogenes (bacteria)
  • streptococcus mutans serotype c (strain atcc 700610 / ua159) (bacteria)
  • yersinia pestis kim10+ (bacteria)
  • pseudomonas aeruginosa (strain pao1) (bacteria)
  • bacillus subtilis (strain 168) (bacteria)
  • streptococcus pneumoniae serotype 4 (strain atcc baa-334 / tigr4) (bacteria)
  • enterobacter cloacae subsp. cloacae atcc 13047 (bacteria)
  • enterococcus faecalis (strain atcc 700802 / v583) (bacteria)
  • yersinia enterocolitica serotype o:8 / biotype 1b (strain nctc 13174 / 8081) (bacteria)
  • pseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) (bacteria)
  • acinetobacter baumannii (strain atcc 19606 / dsm 30007 / cip 70.34 / jcm 6841 / nbrc 109757 / ncimb 12457 / nctc 12156 / 81) (bacteria)
  • enterococcus faecalis v583 (bacteria)
  • burkholderia cenocepacia (strain atcc baa-245 / dsm 16553 / lmg 16656 / nctc 13227 / j2315 / cf5610) (bacteria)
  • bordetella pertussis (bacteria)
  • yersinia enterocolitica subsp. palearctica serotype o:3 (strain dsm 13030 / cip 106945 / y11) (bacteria)
  • streptococcus pyogenes serotype m1 (bacteria)
  • haemophilus influenzae pittii (bacteria)
  • vibrio vulnificus (strain cmcp6) (bacteria)
  • vibrio cholerae serotype o1 (strain atcc 39315 / el tor inaba n16961) (bacteria)
  • aliivibrio fischeri (strain atcc 700601 / es114) (bacteria)
  • bordetella bronchiseptica rb50 (bacteria)
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / dihydrolipoyl dehydrogenase / NUCLEAR PROTEIN / GTP-binding domain / domain II / TRANSFERASE / LIPID BINDING PROTEIN / elongation factor G / Lipid-Binding Protein / Glutathione Reductase / FAD / OXIDOREDUCTASE / alpha-beta structure / TIM barrel / Argininosuccinate Synthase / 7 / 8-dihydropteroate synthase / thioredoxin-disulfide reductase / thioredoxin reductase / Malate Synthase G / Glycolic Acid / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid / (2R)-2-(phosphonooxy)propanoic acid / Magnesium / LIGASE / NIAID / National Institute of Allergy and Infectious Diseases / ALPHA BETA / 3-LAYER(ABA) SANDWICH / ROSSMANN FOLD / NAD SYNTHETASE / 2-oxoglutarate dehydrogenase complex subunit dihydrolipoamide dehydrogenase / Malate Dehydrogenase / Adenosine-5'-monophosphate / D-alanyl-D-alanine Endopeptidase / Boronic Acid. / PHOSPHORIBOSYLTRANSFERASE / 5 / 6-DIMETHYLBENZIMIDAZOLE / NICOTINATE MONONUCLEOTIDE / RIBOSOMAL PROTEIN / L-Malate / Holliday Junction ATP-dependent DNA Helicase / ADP / ISOMERASE / DNA Topoisomerase IV / FAD. / NAD / NadE / AMIDOTRANSFERASE / NH3 DEPENDENT / ATP PYROPHOSPHATASE / oxygen-insensitive nitroreductase / AMP / D-ALANYL-D-ALANINE ENDOPEPTIDASE. / TRANSLATION / Elongation Factor G 2 / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / left-handed beta helix / hexapeptide repeats / beta lactamase class A / Inhibitor / lactamase / serine hydrolase / PenP / CSBID / Center for Structural Biology of Infectious Diseases / Avibactam / clavulonate

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