+Open data
-Basic information
Entry | Database: PDB / ID: 7xld | ||||||||||||||||||
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Title | Crystal structure of IsdH linker-NEAT3 bound to a nanobody (VHH) | ||||||||||||||||||
Components |
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Keywords | METAL TRANSPORT / IsdH system Heme Staphylococcus aureus VHH Nanodoby Antimicrobial | ||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||
Biological species | Staphylococcus aureus (bacteria) Lama glama (llama) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||||||||||||||
Authors | Caaveiro, J.M.M. / Valenciano-Bellido, S. / Tsumoto, K. | ||||||||||||||||||
Funding support | Japan, 5items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth. Authors: Valenciano-Bellido, S. / Caaveiro, J.M.M. / Nakakido, M. / Kuroda, D. / Aikawa, C. / Nakagawa, I. / Tsumoto, K. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xld.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xld.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/7xld ftp://data.pdbj.org/pub/pdb/validation_reports/xl/7xld | HTTPS FTP |
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-Related structure data
Related structure data | 7xliC 3vtmS 4grwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21495.242 Da / Num. of mol.: 1 / Fragment: NEAT3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: isdH, harA, sasI, SAV1731 / Production host: Escherichia coli (E. coli) / References: UniProt: Q931P4 |
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#2: Antibody | Mass: 14967.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-MG / |
#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: 1.91 Å3/Da / Density % sol: 35.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3,350 0.1 M HEPES (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→41 Å / Num. obs: 32081 / % possible obs: 96.1 % / Redundancy: 4.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.65→1.74 Å / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4588 / CC1/2: 0.758 / Rpim(I) all: 0.333 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GRW, 3VTM Resolution: 1.65→40.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.44 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.48 Å2 / Biso mean: 22.047 Å2 / Biso min: 11.28 Å2
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Refinement step | Cycle: final / Resolution: 1.65→40.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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