+Open data
-Basic information
Entry | Database: PDB / ID: 7b3a | ||||||
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Title | Crystal structure of PamZ | ||||||
Components | Putative Acyl-transferase domain protein | ||||||
Keywords | TRANSFERASE / GCN5-RELATED N-ACETYLTRANSFERASE-LIKE PROTEIN / paenilamicin / paenilamicin-gene cluster | ||||||
Function / homology | GNAT acetyltransferase YdfB-like / GNAT acetyltransferase / N-acetyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / ACETATE ION / Putative Acyl-transferase domain protein Function and homology information | ||||||
Biological species | Paenibacillus larvae subsp. larvae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Loll, B. / Dang, T. / Mainz, A. / Suessmuth, R. / Wahl, M.C. | ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Molecular basis of antibiotic self-resistance in a bee larvae pathogen. Authors: Dang, T. / Loll, B. / Muller, S. / Skobalj, R. / Ebeling, J. / Bulatov, T. / Gensel, S. / Gobel, J. / Wahl, M.C. / Genersch, E. / Mainz, A. / Sussmuth, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b3a.cif.gz | 238.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b3a.ent.gz | 161.9 KB | Display | PDB format |
PDBx/mmJSON format | 7b3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b3a_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 7b3a_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 7b3a_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 7b3a_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/7b3a ftp://data.pdbj.org/pub/pdb/validation_reports/b3/7b3a | HTTPS FTP |
-Related structure data
Related structure data | 3g3sS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32271.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus larvae subsp. larvae (bacteria) Gene: ERICIII_02339, ERICV_02787 / Plasmid: pet28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2L1TND5 |
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#2: Chemical | ChemComp-ACO / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 40% (w/v) PEG 3350, 50 mM ammonium sulfate, 100 mM sodium acetate at pH 4.6. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.941841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.941841 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→50 Å / Num. obs: 58898 / % possible obs: 98.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.48 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.068 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.34→1.42 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 9129 / CC1/2: 0.379 / Rrim(I) all: 129.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3G3S Resolution: 1.34→20.2 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.038 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→20.2 Å
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Refine LS restraints |
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LS refinement shell |
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