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Structure paper

TitleA high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.
Journal, issue, pagesMicrobiol Resour Announc, Vol. 12, Page e0050723-e0050723, Year 2023
Publish dateJun 8, 2011 (structure data deposition date)
AuthorsRosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. ...Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / Minor, W. / Joachimiak, A. / Savchenko, A. / Anderson, W.F. / Satchell, K.J.F.
External linksMicrobiol Resour Announc / PubMed:37747257
MethodsX-ray diffraction
Resolution1.5 - 2.702 Å
Structure data

PDB-3sd7:
1.7 Angstrom Resolution Crystal Structure of Putative Phosphatase from Clostridium difficile
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-3srt:
The crystal structure of a maltose O-acetyltransferase from Clostridium difficile 630
Method: X-RAY DIFFRACTION / Resolution: 2.504 Å

PDB-3uuw:
1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium difficile.
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-4gib:
2.27 Angstrom Crystal Structure of beta-Phosphoglucomutase (pgmB) from Clostridium difficile
Method: X-RAY DIFFRACTION / Resolution: 2.27 Å

PDB-4h3d:
1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Modified Comenic Acid.
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-4isx:
The crystal structure of maltose o-acetyltransferase from clostridium difficile 630 in complex with acetyl-coa
Method: X-RAY DIFFRACTION / Resolution: 2.702 Å

PDB-4jjp:
2.06 Angstrom resolution crystal structure of phosphomethylpyrimidine kinase (thiD)from Clostridium difficile 630
Method: X-RAY DIFFRACTION / Resolution: 2.056 Å

PDB-4kd5:
substrate binding domain of putative molybdenum ABC transporter from Clostridium difficile
Method: X-RAY DIFFRACTION / Resolution: 2.4999 Å

PDB-4mfg:
2.0 Angstrom Resolution Crystal Structure of Putative Carbonic Anhydrase from Clostridium difficile.
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-4nmy:
Crystal Structure of the Thiamin-bound form of Substrate-binding Protein of ABC Transporter from Clostridium difficile
Method: X-RAY DIFFRACTION / Resolution: 1.896 Å

PDB-4rn7:
The crystal structure of N-acetylmuramoyl-L-alanine amidase from Clostridium difficile 630
Method: X-RAY DIFFRACTION / Resolution: 1.717 Å

PDB-5dzs:
1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from Peptoclostridium difficile.
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-5tta:
A 1.85A X-Ray Structure from Peptoclostridium difficile 630 of a Hypothetical Protein
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-5tv7:
2.05 Angstrom Resolution Crystal Structure of Peptidoglycan-Binding Protein from Clostridioides difficile in Complex with Glutamine Hydroxamate.
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-5txu:
1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (SpoIID) from Clostridium difficile in Apo Conformation
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-6n7m:
1.78 Angstrom Resolution Crystal Structure of Hypothetical Protein CD630_05490 from Clostridioides difficile 630.
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-6ue2:
1.85 Angstrom Resolution Crystal Structure of Class D beta-lactamase from Clostridium difficile 630
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-6wy4:
Crystal Structure of Wild Type Class D beta-lactamase from Clostridium difficile 630
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7k1u:
Crystal Structure of SrtB-anchored Collagen-binding Adhesin Fragment (residues 206-565) from Clostridioides difficile strain 630
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-7rl8:
Crystal Structure of C79A Mutant of Class D beta-lactamase from Clostridium difficile 630
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-7rlr:
Crystal Structure of K83A Mutant of Class D beta-lactamase from Clostridium difficile 630
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-CL:
Unknown entry

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-GOL:
GLYCEROL

ChemComp-HOH:
WATER

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-1PE:
PENTAETHYLENE GLYCOL / precipitant*YM

ChemComp-PO4:
PHOSPHATE ION

ChemComp-GLY:
GLYCINE

ChemComp-SHL:
5-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxylic acid

ChemComp-ACT:
ACETATE ION

ChemComp-ACO:
ACETYL COENZYME *A

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

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

ChemComp-FMT:
FORMIC ACID

ChemComp-SBT:
2-BUTANOL

ChemComp-SO4:
SULFATE ION

ChemComp-MG:
Unknown entry

ChemComp-NI:
NICKEL (II) ION

ChemComp-VIB:
3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / medication*YM

ChemComp-ZN:
Unknown entry

ChemComp-HGA:
GLUTAMINE HYDROXAMATE

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-PPI:
PROPANOIC ACID

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

ChemComp-EDO:
1,2-ETHANEDIOL

Source
  • clostridium difficile (bacteria)
  • peptoclostridium difficile (bacteria)
  • peptoclostridium difficile (strain 630) (bacteria)
  • clostridioides difficile (strain 630) (bacteria)
  • clostridioides difficile (bacteria)
KeywordsHYDROLASE / Structural Genomics / haloacid dehalogenase-like hydrolase / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSFERASE / maltose O-acetyltransferase / The Center for Structural Genomics of Infectious Diseases / OXIDOREDUCTASE / ISOMERASE / Rossmann fold / HAD-like / beta-Phosphoglucomutase / LYASE / TIM Barrel / Aldolase class I / 3-dehydroquinate dehydratase activity / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / IDP05735 / Biosynthesis of cofactors / prosthetic groups / and carriers: Thiamine / phosphomethylpyrimidine kinase / thiD / Clostridium difficile 630 / virulence / pathogenesis / alpha/beta fold / TRANSPORT PROTEIN / alpha-beta-alpha fold / ABC transporter / Single-stranded left-handed beta-helix / gamma-carbonic anhydrase-like / alpha-beta structure / SBP fold / shikimate dehydrogenase 1 / UNKNOWN FUNCTION / Alpha/Beta protein / Peptidoglycan-Binding Protein / Glutamine Hydroxamate / Hypothetical Protein / blaD / CELL ADHESION / Collagen-binding Adhesin

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