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Open data
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Basic information
Entry | Database: PDB / ID: 7xli | ||||||||||||||||||
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Title | Crystal structure of IsdB linker-NEAT2 bound to a nanobody (VHH) | ||||||||||||||||||
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![]() | METAL TRANSPORT / IsdH system Heme Staphylococcus aureus VHH Nanodoby Antimicrobial | ||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Caaveiro, J.M.M. / Valenciano-Bellido, S. / Tsumoto, K. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.9 KB | Display | ![]() |
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PDB format | ![]() | 86.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7xldSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21177.322 Da / Num. of mol.: 1 / Fragment: NEAT2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: isdB, C7M54_06565, DD547_01151, EP54_07185, EQ90_05325, FAF17_11720, GO814_06830, GO942_06780, GQX37_07535, NCTC13131_00513, SA950122_02636, SAHC1335_02047, SAMEA103891415_00297, SAMEA2076235_ ...Gene: isdB, C7M54_06565, DD547_01151, EP54_07185, EQ90_05325, FAF17_11720, GO814_06830, GO942_06780, GQX37_07535, NCTC13131_00513, SA950122_02636, SAHC1335_02047, SAMEA103891415_00297, SAMEA2076235_00033, SAMEA2078260_00343, SAMEA2078588_00277, SAMEA2078837_01385, SAMEA2080344_00033, SAMEA2081063_00033, SAMEA4008575_00033, SAMEA70146418_01784 Production host: ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-CL / ![]() |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.31 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→40 Å / Num. obs: 31303 / % possible obs: 99.8 % / Redundancy: 8.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.025 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4429 / CC1/2: 0.827 / Rpim(I) all: 0.325 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7XLD Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.417 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 123.02 Å2 / Biso mean: 42.314 Å2 / Biso min: 20.78 Å2
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Refinement step | Cycle: final / Resolution: 1.7→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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