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Yorodumi- PDB-2p4a: X-ray structure of a camelid affinity matured single-domain vhh a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p4a | ||||||
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Title | X-ray structure of a camelid affinity matured single-domain vhh antibody fragment in complex with RNASE A | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / CAMELID SINGLE-DOMAIN ANTIBODY / VHH / CAB-RN05 / RNASE A / PARATOPE / YEAST SURFACE DISPLAY / HYDROLASE-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | Function and homology information immunoglobulin complex / pancreatic ribonuclease / ribonuclease A activity / immunoglobulin mediated immune response / RNA nuclease activity / antigen binding / nucleic acid binding / blood microparticle / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Camelus dromedarius (Arabian camel) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Tereshko, V. / Koide, A. / Uysal, S. / Koide, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope. Authors: Koide, A. / Tereshko, V. / Uysal, S. / Margalef, K. / Kossiakoff, A.A. / Koide, S. | ||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p4a.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p4a.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 2p4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p4a_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
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Full document | 2p4a_full_validation.pdf.gz | 462.9 KB | Display | |
Data in XML | 2p4a_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 2p4a_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/2p4a ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p4a | HTTPS FTP |
-Related structure data
Related structure data | 2p49SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF two VHH-RNASE A COMPLEXes. |
-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 #2: Antibody | Mass: 12830.278 Da / Num. of mol.: 2 / Fragment: TRUNCATED AT RESIDUE 121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) / References: UniProt: A2KD57*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 5.5 Details: HAMPTON RESEARCH INDEX SCREEN, SOLUTION #67, pH 5.5, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 48836 / Num. obs: 48836 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2P49 Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.876 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.127 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.164 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.953 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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