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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 dateJan 27, 2017 (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
Resolution1.5 - 2.72 Å
Structure data

PDB-5ume:
Crystal Structure of 5,10-Methylenetetrahydrofolate Reductase MetF from Haemophilus influenzae
Method: X-RAY DIFFRACTION / Resolution: 2.7 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-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-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-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-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-6c8q:
Crystal structure of NAD synthetase (NadE) from Enterococcus faecalis in complex with NAD+
Method: X-RAY DIFFRACTION / Resolution: 2.583 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

Chemicals

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

ChemComp-SO4:
SULFATE ION

ChemComp-ACY:
ACETIC ACID

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-FMT:
FORMIC ACID

ChemComp-HOH:
WATER

ChemComp-GOL:
GLYCEROL

ChemComp-ACT:
ACETATE ION

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-PO4:
PHOSPHATE ION

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

ChemComp-CL:
Unknown entry

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

ChemComp-MG:
Unknown entry

ChemComp-CA:
Unknown entry

ChemComp-BO4:
BORATE ION

ChemComp-NA:
Unknown entry

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

ChemComp-PGE:
TRIETHYLENE GLYCOL

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

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

Source
  • haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd) (bacteria)
  • vibrio fischeri (strain atcc 700601 / es114) (bacteria)
  • vibrio vulnificus cmcp6 (bacteria)
  • vibrio parahaemolyticus serotype o3:k6 (strain rimd 2210633) (bacteria)
  • streptococcus pyogenes (bacteria)
  • bordetella pertussis (strain tohama i / atcc baa-589 / nctc 13251) (bacteria)
  • enterobacter cloacae subsp. cloacae atcc 13047 (bacteria)
  • yersinia enterocolitica serotype o:8 / biotype 1b (strain nctc 13174 / 8081) (bacteria)
  • enterococcus faecalis (strain atcc 700802 / v583) (bacteria)
  • pseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) (bacteria)
  • enterococcus faecalis v583 (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)
  • bacillus subtilis (strain 168) (bacteria)
KeywordsOXIDOREDUCTASE / alpha-beta structure / TIM barrel / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSFERASE / 7 / 8-dihydropteroate synthase / thioredoxin-disulfide reductase / thioredoxin reductase / 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 / FAD / Malate Dehydrogenase / HYDROLASE / D-alanyl-D-alanine Endopeptidase / Boronic Acid. / PHOSPHORIBOSYLTRANSFERASE / 5 / 6-DIMETHYLBENZIMIDAZOLE / NICOTINATE MONONUCLEOTIDE / RIBOSOMAL PROTEIN / Elongation factor G / Holliday Junction ATP-dependent DNA Helicase / ADP / NAD / NadE / AMIDOTRANSFERASE / NH3 DEPENDENT / ATP PYROPHOSPHATASE / left-handed beta helix / hexapeptide repeats / beta lactamase class A / Inhibitor

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