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- PDB-1bzq: COMPLEX OF A DROMEDARY SINGLE-DOMAIN VHH ANTIBODY FRAGMENT WITH R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bzq | ||||||
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Title | COMPLEX OF A DROMEDARY SINGLE-DOMAIN VHH ANTIBODY FRAGMENT WITH RNASE A | ||||||
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![]() | HYDROLASE/IMMUNE SYSTEM / IMMUNOGLUBULIN / ANTIBODY COMPLEX / RIBONUCLEASE / HYDROLASE-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | ![]() pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Decanniere, K. / Desmyter, A. / Gahroudhi, M. / Lauwereys, M. / Muyldermans, S. / Wyns, L. | ||||||
![]() | ![]() Title: A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops. Authors: Decanniere, K. / Desmyter, A. / Lauwereys, M. / Ghahroudi, M.A. / Muyldermans, S. / Wyns, L. #1: ![]() Title: Crystal Structure of a Camel Single-Domain VH Antibody Fragment in Complex with Lysozyme Authors: Desmyter, A. / Transue, T.R. / Ghahroudi, M.A. / Thi, M.H. / Poortmans, F. / Hmaers, R. / Muyldermans, S. / WYNS, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194 KB | Display | ![]() |
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PDB format | ![]() | 154.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.4 KB | Display | ![]() |
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Full document | ![]() | 532 KB | Display | |
Data in XML | ![]() | 36.5 KB | Display | |
Data in CIF | ![]() | 48.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: RNASE A SUPPLIED BY SIGMA / Source: (natural) ![]() ![]() #2: Antibody | Mass: 13331.775 Da / Num. of mol.: 4 / Fragment: VARIABLE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-PO4 / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 50.77 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.4 Details: HANGING DROP METHOD. 5 MG/ML OF THE COMPLEX RESERVOIR SOLUTION IS 0.1 M POTASSIUM PHOSPHATE PH 6.4 15 TO 20% W/V PEG 8000, vapor diffusion - hanging drop | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15 Å / Num. obs: 25413 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rsym value: 0.111 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.336 / % possible all: 98.2 |
Reflection | *PLUS Rmerge(I) obs: 0.111 |
Reflection shell | *PLUS % possible obs: 98.2 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RUV AND PDB ENTRY 1MEL Resolution: 2.8→20 Å / SU ML: 0.32428 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.45252 Details: CHAINS A, B, C AND D ARE RNASE A MOLECULES CHAINS K, L, M AND N ARE ANTIBODY MOLECULES SEPARATE NCS WAS APPLIED TO EACH GROUP OF MOLECULES
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Displacement parameters | Biso mean: 27.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 25412 / Rfactor all: 0.225 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.224 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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