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Open data
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Basic information
Entry | Database: PDB / ID: 6ksn | |||||||||
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Title | Structure of a Zn-bound camelid single domain antibody | |||||||||
![]() | ICab3 | |||||||||
![]() | METAL BINDING PROTEIN / Indian Camelid Single domain Antibody / VHH | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kumar, S. / Athreya, A. / Penmatsa, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Isolation and structural characterization of a Zn2+-bound single-domain antibody against NorC, a putative multidrug efflux transporter in bacteria. Authors: Kumar, S. / Mahendran, I. / Athreya, A. / Ranjan, R. / Penmatsa, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.8 KB | Display | ![]() |
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PDB format | ![]() | 98.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jbeS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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Components
#1: Protein | Mass: 14662.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.25 / Details: 0.1M Tris, pH8.25, 3.5M Na Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 25502 / % possible obs: 99.6 % / Observed criterion σ(I): 1.9 / Redundancy: 8.9 % / Biso Wilson estimate: 31.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0123 / Rpim(I) all: 0.045 / Rrim(I) all: 0.138 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.15→2.22 Å / Redundancy: 8 % / Rmerge(I) obs: 1.146 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2171 / CC1/2: 0.624 / Rpim(I) all: 0.422 / Rrim(I) all: 1.223 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3JBE Resolution: 2.15→46.28 Å / SU ML: 0.2226 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4642
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→46.28 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.78987484667 Å / Origin y: -42.5000931767 Å / Origin z: 12.0704106222 Å
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Refinement TLS group | Selection details: all |