+Open data
-Basic information
Entry | Database: PDB / ID: 3zqd | |||||||||
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Title | B. subtilis L,D-transpeptidase | |||||||||
Components | L, D-TRANSPEPTIDASE YKUD | |||||||||
Keywords | TRANSFERASE / PEPTIDOGLYCAN / ANTIBIOTIC RESISTANCE / CYSTEINE PROTEASE | |||||||||
Function / homology | Function and homology information spore wall / Transferases / peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / sporulation resulting in formation of a cellular spore / glycosyltransferase activity / cell wall organization / regulation of cell shape / extracellular region Similarity search - Function | |||||||||
Biological species | BACILLUS SUBTILIS SUBSP. SUBTILIS (bacteria) | |||||||||
Method | SOLUTION NMR / ARIA | |||||||||
Authors | Lecoq, L. / Simorre, J.-P. / Bougault, C. / Arthur, M. / Hugonnet, J.-E. / Veckerle, C. / Pessey, O. | |||||||||
Citation | Journal: Structure / Year: 2012 Title: Dynamics Induced by Beta-Lactam Antibiotics in the Active Site of Bacillus subtilis L,D-Transpeptidase. Authors: Lecoq, L. / Bougault, C. / Hugonnet, J. / Veckerle, C. / Pessey, O. / Arthur, M. / Simorre, J. #1: Journal: Proteins / Year: 2006 Title: B. Subtilis Ykud Protein at 2.0 A Resolution: Insights Into the Structure and Function of a Novel, Ubiquitous Family of Bacterial Enzymes. Authors: Bielnicki, J. / Devedjiev, Y. / Derewenda, U. / Dauter, Z. / Joachimiak, A. / Derewenda, Z.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zqd.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3zqd.ent.gz | 925.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zqd ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zqd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 18960.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS (bacteria) Strain: 168 / Plasmid: PET2818 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PREP4GROESL / References: UniProt: O34816 |
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Compound details | HIS 126 IS PROTONATED ON THE ND1 (ND1=ATOM 1950 AND HD1=ATOM 1958) AND NON PROTONATED ON THE NE2 ...HIS 126 IS PROTONATED |
Sequence details | GENE SEQUENCING LED TO THE REPLACEMENT OF THE FIRST MET BY GRKL, AND TO THE ADDITION OF THE C- ...GENE SEQUENCING |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY AND N-H AND CA-HA RDCS ON 13C, 15N-LABELED LDTBS. THE 20 STRUCTURES OF MINIMAL ENERGY WERE FURTHER REFINED IN WATER. |
-Sample preparation
Details | Contents: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 0.15 M / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298.0 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: ARIA / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: MINIMAL ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20 |