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- PDB-2p47: Complex of a camelid single-domain vhh antibody fragment with RNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p47 | ||||||
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Title | Complex of a camelid single-domain vhh antibody fragment with RNASE A at 2.5A resolution: SE5B-TRI crystal form with five se-met sites (L4M, M34, M51, F68M, M83) in vhh scaffold. | ||||||
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![]() | HYDROLASE/IMMUNE SYSTEM / SEMET PHASING / CAMELID SINGLE-DOMAIN ANTIBODY / VHH / CAB-RN05 / RNASE A / YEAST SURFACE DISPLAY. / HYDROLASE / 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 | ![]() ![]() ![]() | ||||||
![]() | Tereshko, V. / Uysal, S. / Koide, A. / Margalef, K. / Koide, S. / Kossiakoff, A.A. | ||||||
![]() | ![]() Title: Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold Authors: Tereshko, V. / Uysal, S. / Koide, A. / Margalef, K. / Koide, S. / Kossiakoff, A.A. | ||||||
History |
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Remark 999 | SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF VHH ANTIBODY IS NOT AVAILABLE AT THE UNP ...SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF VHH ANTIBODY IS NOT AVAILABLE AT THE UNP SEQUENCE DATABASE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.1 KB | Display | ![]() |
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PDB format | ![]() | 43.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 447.6 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2p42C ![]() 2p43C ![]() 2p44C ![]() 2p45SC ![]() 2p46C ![]() 2p48C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE VHH-RNASE A COMPLEX. EACH COMPLEX CONSISTS OF TWO CHAINS, A AND B, AND REPRESENTS ONE BIOLOGICAL UNIT. |
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Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 13341.001 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 Details: HAMPTON RESEARCH INDEX SCREEN, SOLUTION #68: (NH4)SO4, PEG 3350, HEPES BUFFER, PH 7.5, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 1, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 10142 / Num. obs: 10142 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 2P45 Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU B: 39.129 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.4 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.208 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / 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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